Online Searching with a Microcomputer--Getting Started.

ERIC Educational Resources Information Center

Casbon, Susan

1983-01-01

Based on online searching experiences on microcomputer at a small liberal arts college, this article outlines for the novice advantages and disadvantages of micro-searching, legal implications, future trends, and factors to consider in selecting hardware and software. A 16-item bibliography arranged in order of usefulness and 10 references are…

The Job Search Goes Computer.

ERIC Educational Resources Information Center

Kennedy, Joyce Lain

1994-01-01

Discusses significant new developments in the electronic search process: (1) New Government Automation; (2) New Federal Initiatives; (3) New Telecommunications Services; (4) Campus Data Bases; (5) Off-Campus Data Bases; (6) Faxed or E-Mailed Resumes; (7) Automation of 3rd-Party Recruiters; (8) New Cyberservices; (9) Interview-Prep Software; (10)…

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

Evidence of absence (v2.0) software user guide

USGS Publications Warehouse

Dalthorp, Daniel; Huso, Manuela; Dail, David

2017-07-06

Evidence of Absence software (EoA) is a user-friendly software application for estimating bird and bat fatalities at wind farms and for designing search protocols. The software is particularly useful in addressing whether the number of fatalities is below a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The software also includes tools (1) for estimating carcass persistence distributions and searcher efficiency parameters ( and ) from field trials, (2) for projecting future mortality based on past monitoring data, and (3) for exploring the potential consequences of various choices in the design of long-term incidental take permits for protected species. The software was designed specifically for cases where tolerance for mortality is low and carcass counts are small or even 0, but the tools also may be used for mortality estimates when carcass counts are large.

NLM microcomputer-based tutorials (for microcomputers). Software

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

Perkins, M.

1990-04-01

The package consists of TOXLEARN--a microcomputer-based training package for TOXLINE (Toxicology Information Online), CHEMLEARN-a microcomputer-based training package for CHEMLINE (Chemical Information Online), MEDTUTOR--a microcomputer-based training package for MEDLINE (Medical Information Online), and ELHILL LEARN--a microcomputer-based training package for the ELHILL search and retrieval software that supports the above-mentioned databases...Software Description: The programs were developed under PILOTplus using the NLM LEARN Programmer. They run on IBM-PC, XT, AT, PS/2, and fully compatible computers. The programs require 512K RAM memory, one disk drive, and DOS 2.0 or higher. The software supports most monochrome, color graphics, enhanced color graphics, or visual graphics displays.

Mercury: An Example of Effective Software Reuse for Metadata Management, Data Discovery and Access

NASA Astrophysics Data System (ADS)

Devarakonda, Ranjeet; Palanisamy, Giri; Green, James; Wilson, Bruce E.

2008-12-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. Though originally developed for NASA, the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the 12 projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects. To balance these common and project-specific needs, Mercury's architecture has three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of project specific configuration files. The harvested files are structured metadata records that are indexed against the search library API consistently, so that it can render various search capabilities such as simple, fielded, spatial and temporal. This backend component is supported by a very flexible, easy to use Graphical User Interface which is driven by cascading style sheets, which make it even simpler for reusable design implementation. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book- markable search results, save, retrieve, and modify search criteria.

Mercury: An Example of Effective Software Reuse for Metadata Management, Data Discovery and Access

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

Devarakonda, Ranjeet

2008-01-01

Mercury is a federated metadata harvesting, data discovery and access tool based on both open source packages and custom developed software. Though originally developed for NASA, the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports the reuse of metadata by enabling searching across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. Mercury provides a single portal to information contained in distributed data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfacesmore » then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. One of the major goals of the recent redesign of Mercury was to improve the software reusability across the 12 projects which currently fund the continuing development of Mercury. These projects span a range of land, atmosphere, and ocean ecological communities and have a number of common needs for metadata searches, but they also have a number of needs specific to one or a few projects. To balance these common and project-specific needs, Mercury's architecture has three major reusable components; a harvester engine, an indexing system and a user interface component. The harvester engine is responsible for harvesting metadata records from various distributed servers around the USA and around the world. The harvester software was packaged in such a way that all the Mercury projects will use the same harvester scripts but each project will be driven by a set of project specific configuration files. The harvested files are structured metadata records that are indexed against the search library API consistently, so that it can render various search capabilities such as simple, fielded, spatial and temporal. This backend component is supported by a very flexible, easy to use Graphical User Interface which is driven by cascading style sheets, which make it even simpler for reusable design implementation. The new Mercury system is based on a Service Oriented Architecture and effectively reuses components for various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. The software also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets, integrated shopping cart to order datasets from various data centers (ORNL DAAC, NSIDC) and integrated visualization tools. Other features include: Filtering and dynamic sorting of search results, book- markable search results, save, retrieve, and modify search criteria.« less

Spatial Query for Planetary Data

NASA Technical Reports Server (NTRS)

Shams, Khawaja S.; Crockett, Thomas M.; Powell, Mark W.; Joswig, Joseph C.; Fox, Jason M.

2011-01-01

Science investigators need to quickly and effectively assess past observations of specific locations on a planetary surface. This innovation involves a location-based search technology that was adapted and applied to planetary science data to support a spatial query capability for mission operations software. High-performance location-based searching requires the use of spatial data structures for database organization. Spatial data structures are designed to organize datasets based on their coordinates in a way that is optimized for location-based retrieval. The particular spatial data structure that was adapted for planetary data search is the R+ tree.

An open source software for fast grid-based data-mining in spatial epidemiology (FGBASE).

PubMed

Baker, David M; Valleron, Alain-Jacques

2014-10-30

Examining whether disease cases are clustered in space is an important part of epidemiological research. Another important part of spatial epidemiology is testing whether patients suffering from a disease are more, or less, exposed to environmental factors of interest than adequately defined controls. Both approaches involve determining the number of cases and controls (or population at risk) in specific zones. For cluster searches, this often must be done for millions of different zones. Doing this by calculating distances can lead to very lengthy computations. In this work we discuss the computational advantages of geographical grid-based methods, and introduce an open source software (FGBASE) which we have created for this purpose. Geographical grids based on the Lambert Azimuthal Equal Area projection are well suited for spatial epidemiology because they preserve area: each cell of the grid has the same area. We describe how data is projected onto such a grid, as well as grid-based algorithms for spatial epidemiological data-mining. The software program (FGBASE), that we have developed, implements these grid-based methods. The grid based algorithms perform extremely fast. This is particularly the case for cluster searches. When applied to a cohort of French Type 1 Diabetes (T1D) patients, as an example, the grid based algorithms detected potential clusters in a few seconds on a modern laptop. This compares very favorably to an equivalent cluster search using distance calculations instead of a grid, which took over 4 hours on the same computer. In the case study we discovered 4 potential clusters of T1D cases near the cities of Le Havre, Dunkerque, Toulouse and Nantes. One example of environmental analysis with our software was to study whether a significant association could be found between distance to vineyards with heavy pesticide. None was found. In both examples, the software facilitates the rapid testing of hypotheses. Grid-based algorithms for mining spatial epidemiological data provide advantages in terms of computational complexity thus improving the speed of computations. We believe that these methods and this software tool (FGBASE) will lower the computational barriers to entry for those performing epidemiological research.

Database Search Engines: Paradigms, Challenges and Solutions.

PubMed

Verheggen, Kenneth; Martens, Lennart; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

The first step in identifying proteins from mass spectrometry based shotgun proteomics data is to infer peptides from tandem mass spectra, a task generally achieved using database search engines. In this chapter, the basic principles of database search engines are introduced with a focus on open source software, and the use of database search engines is demonstrated using the freely available SearchGUI interface. This chapter also discusses how to tackle general issues related to sequence database searching and shows how to minimize their impact.

Choice: 36 band feature selection software with applications to multispectral pattern recognition

NASA Technical Reports Server (NTRS)

Jones, W. C.

1973-01-01

Feature selection software was developed at the Earth Resources Laboratory that is capable of inputting up to 36 channels and selecting channel subsets according to several criteria based on divergence. One of the criterion used is compatible with the table look-up classifier requirements. The software indicates which channel subset best separates (based on average divergence) each class from all other classes. The software employs an exhaustive search technique, and computer time is not prohibitive. A typical task to select the best 4 of 22 channels for 12 classes takes 9 minutes on a Univac 1108 computer.

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.

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.

PubMed

Muth, Thilo; Kohrs, Fabian; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Reichl, Udo; Martens, Lennart; Renard, Bernhard Y

2018-01-02

Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks. While search engine results can easily be combined to increase the protein identification yield, an additional two-step workflow is implemented to provide sufficient analysis resolution for further postprocessing steps, such as protein grouping as well as taxonomic and functional annotation. Our new application has been developed with a focus on intuitive usability, adherence to data standards, and adaptation to Web-based workflow platforms. The open source software package can be found at https://github.com/compomics/meta-proteome-analyzer .

Software Framework for Peer Data-Management Services

NASA Technical Reports Server (NTRS)

Hughes, John; Hardman, Sean; Crichton, Daniel; Hyon, Jason; Kelly, Sean; Tran, Thuy

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-to-peer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

A pluggable framework for parallel pairwise sequence search.

PubMed

Archuleta, Jeremy; Feng, Wu-chun; Tilevich, Eli

2007-01-01

The current and near future of the computing industry is one of multi-core and multi-processor technology. Most existing sequence-search tools have been designed with a focus on single-core, single-processor systems. This discrepancy between software design and hardware architecture substantially hinders sequence-search performance by not allowing full utilization of the hardware. This paper presents a novel framework that will aid the conversion of serial sequence-search tools into a parallel version that can take full advantage of the available hardware. The framework, which is based on a software architecture called mixin layers with refined roles, enables modules to be plugged into the framework with minimal effort. The inherent modular design improves maintenance and extensibility, thus opening up a plethora of opportunities for advanced algorithmic features to be developed and incorporated while routine maintenance of the codebase persists.

Improving Target Detection in Visual Search Through the Augmenting Multi-Sensory Cues

DTIC Science & Technology

2013-01-01

target detection, visual search James Merlo, Joseph E. Mercado , Jan B.F. Van Erp, Peter A. Hancock University of Central Florida 12201 Research Parkway...were controlled by a purpose-created, LabView- based software computer program that synchronised the respective displays and recorded response times and

BIOREMEDIATION IN THE FIELD SEARCH SYSTEM (BFSS) - VERSION 2.0 (DISKETTE)

EPA Science Inventory

BFSS is a PC-based software product that provides access to a database of information on waste sites in the United States and Canada where bioremediation is being tested or implemented, or has been completed. BFSS allows users to search the database electronically, view data on s...

Are Bibliographic Management Software Search Interfaces Reliable?: A Comparison between Search Results Obtained Using Database Interfaces and the EndNote Online Search Function

ERIC Educational Resources Information Center

Fitzgibbons, Megan; Meert, Deborah

2010-01-01

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search…

Development of program package for investigation and modeling of carbon nanostructures in diamond like carbon films with the help of Raman scattering and infrared absorption spectra line resolving

NASA Astrophysics Data System (ADS)

Hayrapetyan, David B.; Hovhannisyan, Levon; Mantashyan, Paytsar A.

2013-04-01

The analysis of complex spectra is an actual problem for modern science. The work is devoted to the creation of a software package, which analyzes spectrum in the different formats, possesses by dynamic knowledge database and self-study mechanism, performs automated analysis of the spectra compound based on knowledge database by application of certain algorithms. In the software package as searching systems, hyper-spherical random search algorithms, gradient algorithms and genetic searching algorithms were used. The analysis of Raman and IR spectrum of diamond-like carbon (DLC) samples were performed by elaborated program. After processing the data, the program immediately displays all the calculated parameters of DLC.

Enhanced Visualization of Subtle Outer Retinal Pathology by En Face Optical Coherence Tomography and Correlation with Multi-Modal Imaging

PubMed Central

Chew, Avenell L.; Lamey, Tina; McLaren, Terri; De Roach, John

2016-01-01

Purpose To present en face optical coherence tomography (OCT) images generated by graph-search theory algorithm-based custom software and examine correlation with other imaging modalities. Methods En face OCT images derived from high density OCT volumetric scans of 3 healthy subjects and 4 patients using a custom algorithm (graph-search theory) and commercial software (Heidelberg Eye Explorer software (Heidelberg Engineering)) were compared and correlated with near infrared reflectance, fundus autofluorescence, adaptive optics flood-illumination ophthalmoscopy (AO-FIO) and microperimetry. Results Commercial software was unable to generate accurate en face OCT images in eyes with retinal pigment epithelium (RPE) pathology due to segmentation error at the level of Bruch’s membrane (BM). Accurate segmentation of the basal RPE and BM was achieved using custom software. The en face OCT images from eyes with isolated interdigitation or ellipsoid zone pathology were of similar quality between custom software and Heidelberg Eye Explorer software in the absence of any other significant outer retinal pathology. En face OCT images demonstrated angioid streaks, lesions of acute macular neuroretinopathy, hydroxychloroquine toxicity and Bietti crystalline deposits that correlated with other imaging modalities. Conclusions Graph-search theory algorithm helps to overcome the limitations of outer retinal segmentation inaccuracies in commercial software. En face OCT images can provide detailed topography of the reflectivity within a specific layer of the retina which correlates with other forms of fundus imaging. Our results highlight the need for standardization of image reflectivity to facilitate quantification of en face OCT images and longitudinal analysis. PMID:27959968

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NASA Technical Reports Server (NTRS)

Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

2006-01-01

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

Software for Project-Based Learning of Robot Motion Planning

ERIC Educational Resources Information Center

Moll, Mark; Bordeaux, Janice; Kavraki, Lydia E.

2013-01-01

Motion planning is a core problem in robotics concerned with finding feasible paths for a given robot. Motion planning algorithms perform a search in the high-dimensional continuous space of robot configurations and exemplify many of the core algorithmic concepts of search algorithms and associated data structures. Motion planning algorithms can…

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

Peeling the Onion: Okapi System Architecture and Software Design Issues.

ERIC Educational Resources Information Center

Jones, S.; And Others

1997-01-01

Discusses software design issues for Okapi, an information retrieval system that incorporates both search engine and user interface and supports weighted searching, relevance feedback, and query expansion. The basic search system, adjacency searching, and moving toward a distributed system are discussed. (Author/LRW)

Software - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You are here: Home › USNO › Earth Orientation › Software USNO Logo USNO Navigation Earth Orientation Search databases Auxiliary Software Supporting Software Form Folder Earth Orientation Matrix Calculator

Design and Empirical Evaluation of Search Software for Legal Professionals on the WWW.

ERIC Educational Resources Information Center

Dempsey, Bert J.; Vreeland, Robert C.; Sumner, Robert G., Jr.; Yang, Kiduk

2000-01-01

Discussion of effective search aids for legal researchers on the World Wide Web focuses on the design and evaluation of two software systems developed to explore models for browsing and searching across a user-selected set of Web sites. Describes crawler-enhanced search engines, filters, distributed full-text searching, and natural language…

MAIL LOG, program summary and specifications

NASA Technical Reports Server (NTRS)

Harris, D. K.

1979-01-01

The summary and specifications to obtain the software package, MAIL LOG, developed for the Scout Project Automatic Data System, SPADS are provided. The MAIL LOG program has four modes of operation: (1) input - putting new records into the data base; (2) revise - changing or modifying existing records in the data base; (3) search - finding special records existing in the data base; and (4) archive - store or put away existing records in the data base. The output includes special printouts of records in the data base and results from the input and search modes.

Software for project-based learning of robot motion planning

NASA Astrophysics Data System (ADS)

Moll, Mark; Bordeaux, Janice; Kavraki, Lydia E.

2013-12-01

Motion planning is a core problem in robotics concerned with finding feasible paths for a given robot. Motion planning algorithms perform a search in the high-dimensional continuous space of robot configurations and exemplify many of the core algorithmic concepts of search algorithms and associated data structures. Motion planning algorithms can be explained in a simplified two-dimensional setting, but this masks many of the subtleties and complexities of the underlying problem. We have developed software for project-based learning of motion planning that enables deep learning. The projects that we have developed allow advanced undergraduate students and graduate students to reflect on the performance of existing textbook algorithms and their own variations on such algorithms. Formative assessment has been conducted at three institutions. The core of the software used for this teaching module is also used within the Robot Operating System, a widely adopted platform by the robotics research community. This allows for transfer of knowledge and skills to robotics research projects involving a large variety robot hardware platforms.

VSO For Dummies

NASA Astrophysics Data System (ADS)

Schwartz, Richard A.; Zarro, D.; Csillaghy, A.; Dennis, B.; Tolbert, A. K.; Etesi, L.

2009-05-01

We report on our activities to integrate VSO search and retrieval capabilities into standard data access, display, and analysis tools. In addition to its standard Web-based search form, the VSO provides an Interactive Data Language (IDL) client (vso_search) that is available through the Solar Software (SSW) package. We have incorporated this client into an IDL-widget interface program (show_synop) that allows for more simplified searching and downloading of VSO datasets directly into a user's IDL data analysis environment. In particular, we have provided the capability to read VSO datasets into a general purpose IDL package (plotman) that can display different datatypes (lightcurves, images, and spectra) and perform basic data operations such as zooming, image overlays, solar rotation, etc. Currently, the show_synop tool supports access to ground-based and space-based (SOHO, STEREO, and Hinode) observations, and has the capability to include new datasets as they become available. A user encounters two major hurdles when using the VSO: (1) Instrument-specific software (such as level-0 file readers and data-prepping procedures) may not be available in the user's local SSW distribution. (2) Recent calibration files (such as flat-fields) are not automatically distributed with the analysis software. To address these issues, we have developed a dedicated server (prepserver) that incorporates all the latest instrument-specific software libraries and calibration files. The prepserver uses an IDL-Java bridge to read and implement data processing requests from a client and return a processed data file that can be readily displayed with the show_synop/plotman package. The advantage of the prepserver is that the user is only required to install the general branch (gen) of the SSW tree, and is freed from the more onerous task of installing instrument-specific libraries and calibration files. We will demonstrate how the prepserver can be used to read, process, and overlay SOHO/EIT, TRACE, SECCHI/EUVI, and RHESSI images.

Using dBASE II for Bibliographic Files.

ERIC Educational Resources Information Center

Sullivan, Jeanette

1985-01-01

Describes use of a database management system (dBASE II, produced by Ashton-Tate), noting best features and disadvantages. Highlights include data entry, multiple access points available, training requirements, use of dBASE for a bibliographic application, auxiliary software, and dBASE updates. Sample searches, auxiliary programs, and requirements…

Environmental Information Management For Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Giriprakash, P.

2011-01-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source software and software developed at Oak Ridge National Laboratory. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. A major new version of Mercury was developed during 2007 and released in early 2008. This new version provides orders of magnitude improvements in search speed, support for additional metadata formats, integration with Google Maps for spatial queries, support for RSS delivery of search results, and ready customization to meet the needs of the multiple projects which use Mercury. For the end users, Mercury provides a single portal to very quickly search for data and information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow ! the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data.

Evidence of Absence software

USGS Publications Warehouse

Dalthorp, Daniel; Huso, Manuela M. P.; Dail, David; Kenyon, Jessica

2014-01-01

Evidence of Absence software (EoA) is a user-friendly application used for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The software is applicable even when zero carcasses have been found in searches. Depending on the effectiveness of the searches, such an absence of evidence of mortality may or may not be strong evidence that few fatalities occurred. Under a search protocol in which carcasses are detected with nearly 100 percent certainty, finding zero carcasses would be convincing evidence that overall mortality rate was near zero. By contrast, with a less effective search protocol with low probability of detecting a carcass, finding zero carcasses does not rule out the possibility that large numbers of animals were killed but not detected in the searches. EoA uses information about the search process and scavenging rates to estimate detection probabilities to determine a maximum credible number of fatalities, even when zero or few carcasses are observed.

Tracking-Data-Conversion Tool

NASA Technical Reports Server (NTRS)

Flora-Adams, Dana; Makihara, Jeanne; Benenyan, Zabel; Berner, Jeff; Kwok, Andrew

2007-01-01

Object Oriented Data Technology (OODT) is a software framework for creating a Web-based system for exchange of scientific data that are stored in diverse formats on computers at different sites under the management of scientific peers. OODT software consists of a set of cooperating, distributed peer components that provide distributed peer-topeer (P2P) services that enable one peer to search and retrieve data managed by another peer. In effect, computers running OODT software at different locations become parts of an integrated data-management system.

Software Supportability Risk Assessment in OT&E (Operational Test and Evaluation): Literature Review, Current Research Review, and Data Base Assemblage.

DTIC Science & Technology

1984-09-28

variables before simula- tion of model - Search for reality checks a, - Express uncertainty as a probability density distribution. a. H2 a, H-22 TWIF... probability that the software con- tains errors. This prior is updated as test failure data are accumulated. Only a p of 1 (software known to contain...discusssed; both parametric and nonparametric versions are presented. It is shown by the author that the bootstrap underlies the jackknife method and

Front-End/Gateway Software: Availability and Usefulness.

ERIC Educational Resources Information Center

Kesselman, Martin

1985-01-01

Reviews features of front-end software packages (interface between user and online system)--database selection, search strategy development, saving and downloading, hardware and software requirements, training and documentation, online systems and database accession, and costs--and discusses gateway services (user searches through intermediary…

31 CFR 560.538 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for reading, browsing, navigating, or searching a written publication in electronic format, provided that the software...

31 CFR 560.538 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2011 CFR

2011-07-01

... publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for reading, browsing, navigating, or searching a written publication in electronic format, provided that the software...

The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

PubMed

Chen, Yi-Bu; Chattopadhyay, Ansuman; Bergen, Phillip; Gadd, Cynthia; Tannery, Nancy

2007-01-01

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Sciences Library System (HSLS) at the University of Pittsburgh. The OBRC, containing 1542 major online bioinformatics databases and software tools, was constructed using the HSLS content management system built on the Zope Web application server. To enhance the output of search results, we further implemented the Vivísimo Clustering Engine, which automatically organizes the search results into categories created dynamically based on the textual information of the retrieved records. As the largest online collection of its kind and the only one with advanced search results clustering, OBRC is aimed at becoming a one-stop guided information gateway to the major bioinformatics databases and software tools on the Web. OBRC is available at the University of Pittsburgh's HSLS Web site (http://www.hsls.pitt.edu/guides/genetics/obrc).

Algorithms for database-dependent search of MS/MS data.

PubMed

Matthiesen, Rune

2013-01-01

The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather than providing software user manuals. The process of database-dependent search can be divided into search strategy, peptide scoring, protein scoring, and finally protein inference. Most efforts in the literature have been put in to comparing results from different software rather than discussing the underlining algorithms. Such practical comparisons can be cluttered by suboptimal implementation and the observed differences are frequently caused by software parameters settings which have not been set proper to allow even comparison. In other words an algorithmic idea can still be worth considering even if the software implementation has been demonstrated to be suboptimal. The aim in this chapter is therefore to split the algorithms for database-dependent searching of MS/MS data into the above steps so that the different algorithmic ideas become more transparent and comparable. Most search engines provide good implementations of the first three data analysis steps mentioned above, whereas the final step of protein inference are much less developed for most search engines and is in many cases performed by an external software. The final part of this chapter illustrates how protein inference is built into the VEMS search engine and discusses a stand-alone program SIR for protein inference that can import a Mascot search result.

A Novel Method for Mining SaaS Software Tag via Community Detection in Software Services Network

NASA Astrophysics Data System (ADS)

Qin, Li; Li, Bing; Pan, Wei-Feng; Peng, Tao

The number of online software services based on SaaS paradigm is increasing. However, users usually find it hard to get the exact software services they need. At present, tags are widely used to annotate specific software services and also to facilitate the searching of them. Currently these tags are arbitrary and ambiguous since mostly of them are generated manually by service developers. This paper proposes a method for mining tags from the help documents of software services. By extracting terms from the help documents and calculating the similarity between the terms, we construct a software similarity network where nodes represent software services, edges denote the similarity relationship between software services, and the weights of the edges are the similarity degrees. The hierarchical clustering algorithm is used for community detection in this software similarity network. At the final stage, tags are mined for each of the communities and stored as ontology.

Locating Biodiversity Data Through The Global Change Master Directory

NASA Technical Reports Server (NTRS)

Olsen, Lola M.

1998-01-01

The Global Change Master Directory (GCMD) presently holds descriptions for almost 7000 data sets held worldwide. The directory's primary purpose is for data discovery. The information provided through the GCMD's Directory Interchange Format (DIF) is the set of information that a researcher would need to determine if a particular data set could be of value. By offering data set descriptions worldwide in many scientific disciplines - including meteorology, oceanography, ecology, geology, hydrology, geophysics, remote sensing, paleoclimate, solar-terrestrial physics, and human dimensions of climate change - the GCMD simplifies the discovery of data sources. Direct linkages to many of the data sets are also provided. In addition, several data set registration tools are offered for populating the directory. To search the directory, one may choose the Guided Search or Free-Text Search. Two experimental interfaces were also made available with the latest software release - one based on a keyword search and another based on a graphical interface. The graphical interface was designed in collaboration with the Human Computer Interaction Laboratory at the University of Maryland. The latest version of the software, Version 6, was released in April, 1998. It features the implementation of a scheme to handle hierarchical data set collections (parent-child relationships); a hierarchical geospatial location search scheme; a Java-based geographic map for conducting geospatial searches; a Related-URL field for project-related data set collections, metadata extensions (such as more detailed inventory information), etc.; a new implementation of the Isite software; a new dataset language field; hyperlinked email addresses, and more. The key to the continued evolution of the GCMD is in the flexibility of the GCMD database, allowing modifications and additions to made relatively easily to maintain currency, thus providing the ability to capitalize on current technology while importing all existing records. Changes are discussed and approved through an online "interoperability" forum. The next major release of the GCMD is scheduled for early 1999 and will include the incorporation of a new matrix-based interface, a rapid valids-based query system; improvement in the operations facility - important for future distributed options; new streamlined code for greater performance and maintainability; improvements in the handling of seven current fields proposed through the interoperability forum (at no expense to the data providers); and the release of DOCmorph, a more robust version of DIFmorph to translate many 'standards' multi-directionally. Issues and actions will also be addressed.

Web-Based Environment for Maintaining Legacy Software

NASA Technical Reports Server (NTRS)

Tigges, Michael; Thompson, Nelson; Orr, Mark; Fox, Richard

2007-01-01

Advanced Tool Integration Environment (ATIE) is the name of both a software system and a Web-based environment created by the system for maintaining an archive of legacy software and expertise involved in developing the legacy software. ATIE can also be used in modifying legacy software and developing new software. The information that can be encapsulated in ATIE includes experts documentation, input and output data of tests cases, source code, and compilation scripts. All of this information is available within a common environment and retained in a database for ease of access and recovery by use of powerful search engines. ATIE also accommodates the embedment of supporting software that users require for their work, and even enables access to supporting commercial-off-the-shelf (COTS) software within the flow of the experts work. The flow of work can be captured by saving the sequence of computer programs that the expert uses. A user gains access to ATIE via a Web browser. A modern Web-based graphical user interface promotes efficiency in the retrieval, execution, and modification of legacy code. Thus, ATIE saves time and money in the support of new and pre-existing programs.

Querying archetype-based EHRs by search ontology-based XPath engineering.

PubMed

Kropf, Stefan; Uciteli, Alexandr; Schierle, Katrin; Krücken, Peter; Denecke, Kerstin; Herre, Heinrich

2018-05-11

Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards. The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist. The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.

Data-Base Software For Tracking Technological Developments

NASA Technical Reports Server (NTRS)

Aliberti, James A.; Wright, Simon; Monteith, Steve K.

1996-01-01

Technology Tracking System (TechTracS) computer program developed for use in storing and retrieving information on technology and related patent information developed under auspices of NASA Headquarters and NASA's field centers. Contents of data base include multiple scanned still images and quick-time movies as well as text. TechTracS includes word-processing, report-editing, chart-and-graph-editing, and search-editing subprograms. Extensive keyword searching capabilities enable rapid location of technologies, innovators, and companies. System performs routine functions automatically and serves multiple users.

Federating Metadata Catalogs

NASA Astrophysics Data System (ADS)

Baru, C.; Lin, K.

2009-04-01

The Geosciences Network project (www.geongrid.org) has been developing cyberinfrastructure for data sharing in the Earth Science community based on a service-oriented architecture. The project defines a standard "software stack", which includes a standardized set of software modules and corresponding service interfaces. The system employs Grid certificates for distributed user authentication. The GEON Portal provides online access to these services via a set of portlets. This service-oriented approach has enabled the GEON network to easily expand to new sites and deploy the same infrastructure in new projects. To facilitate interoperation with other distributed geoinformatics environments, service standards are being defined and implemented for catalog services and federated search across distributed catalogs. The need arises because there may be multiple metadata catalogs in a distributed system, for example, for each institution, agency, geographic region, and/or country. Ideally, a geoinformatics user should be able to search across all such catalogs by making a single search request. In this paper, we describe our implementation for such a search capability across federated metadata catalogs in the GEON service-oriented architecture. The GEON catalog can be searched using spatial, temporal, and other metadata-based search criteria. The search can be invoked as a Web service and, thus, can be imbedded in any software application. The need for federated catalogs in GEON arises because, (i) GEON collaborators at the University of Hyderabad, India have deployed their own catalog, as part of the iGEON-India effort, to register information about local resources for broader access across the network, (ii) GEON collaborators in the GEO Grid (Global Earth Observations Grid) project at AIST, Japan have implemented a catalog for their ASTER data products, and (iii) we have recently deployed a search service to access all data products from the EarthScope project in the US (http://es-portal.geongrid.org), which are distributed across data archives at IRIS in Seattle, Washington, UNAVCO in Boulder, Colorado, and at the ICDP archives in GFZ, Potsdam, Germany. This service implements a "virtual" catalog--the actual/"physical" catalogs and data are stored at each of the remote locations. A federated search across all these catalogs would enable GEON users to discover data across all of these environments with a single search request. Our objective is to implement this search service via the OGC Catalog Services for the Web (CS-W) standard by providing appropriate CSW "wrappers" for each metadata catalog, as necessary. This paper will discuss technical issues in designing and deploying such a multi-catalog search service in GEON and describe an initial prototype of the federated search capability.

Seqcrawler: biological data indexing and browsing platform.

PubMed

Sallou, Olivier; Bretaudeau, Anthony; Roult, Aurelien

2012-07-24

Seqcrawler takes its roots in software like SRS or Lucegene. It provides an indexing platform to ease the search of data and meta-data in biological banks and it can scale to face the current flow of data. While many biological bank search tools are available on the Internet, mainly provided by large organizations to search their data, there is a lack of free and open source solutions to browse one's own set of data with a flexible query system and able to scale from a single computer to a cloud system. A personal index platform will help labs and bioinformaticians to search their meta-data but also to build a larger information system with custom subsets of data. The software is scalable from a single computer to a cloud-based infrastructure. It has been successfully tested in a private cloud with 3 index shards (pieces of index) hosting ~400 millions of sequence information (whole GenBank, UniProt, PDB and others) for a total size of 600 GB in a fault tolerant architecture (high-availability). It has also been successfully integrated with software to add extra meta-data from blast results to enhance users' result analysis. Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface. All components (search engine, visualization and data storage), though independent, share a common and coherent data system that can be queried with a simple HTTP interface. The solution scales easily and can also provide a high availability infrastructure.

Software and package applicating for network meta-analysis: A usage-based comparative study.

PubMed

Xu, Chang; Niu, Yuming; Wu, Junyi; Gu, Huiyun; Zhang, Chao

2017-12-21

To compare and analyze the characteristics and functions of software applications for network meta-analysis (NMA). PubMed, EMbase, The Cochrane Library, the official websites of Bayesian inference Using Gibbs Sampling (BUGS), Stata and R, and Google were searched to collect the software and packages for performing NMA; software and packages published up to March 2016 were included. After collecting the software, packages, and their user guides, we used the software and packages to calculate a typical example. All characteristics, functions, and computed results were compared and analyzed. Ten types of software were included, including programming and non-programming software. They were developed mainly based on Bayesian or frequentist theory. Most types of software have the characteristics of easy operation, easy mastery, exact calculation, or excellent graphing. However, there was no single software that performed accurate calculations with superior graphing; this could only be achieved through the combination of two or more types of software. This study suggests that the user should choose the appropriate software according to personal programming basis, operational habits, and financial ability. Then, the choice of the combination of BUGS and R (or Stata) software to perform the NMA is considered. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Frequency Estimator Performance for a Software-Based Beacon Receiver

NASA Technical Reports Server (NTRS)

Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.; Miranda, Felix

2014-01-01

As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a QV-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

PubMed

Khashan, Raed S

2015-01-01

As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

Development of preoperative planning software for transforaminal endoscopic surgery and the guidance for clinical applications.

PubMed

Chen, Xiaojun; Cheng, Jun; Gu, Xin; Sun, Yi; Politis, Constantinus

2016-04-01

Preoperative planning is of great importance for transforaminal endoscopic techniques applied in percutaneous endoscopic lumbar discectomy. In this study, a modular preoperative planning software for transforaminal endoscopic surgery was developed and demonstrated. The path searching method is based on collision detection, and the oriented bounding box was constructed for the anatomical models. Then, image reformatting algorithms were developed for multiplanar reconstruction which provides detailed anatomical information surrounding the virtual planned path. Finally, multithread technique was implemented to realize the steady-state condition of the software. A preoperative planning software for transforaminal endoscopic surgery (TE-Guider) was developed; seven cases of patients with symptomatic lumbar disc herniations were planned preoperatively using TE-Guider. The distances to the midlines and the direction of the optimal paths were exported, and each result was in line with the empirical value. TE-Guider provides an efficient and cost-effective way to search the ideal path and entry point for the puncture. However, more clinical cases will be conducted to demonstrate its feasibility and reliability.

The widest practicable dissemination: The NASA technical report server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Binkley, Robert L.; Kellogg, Yvonne D.; Paulson, Sharon S.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael; Accomazzi, Alberto

1995-01-01

The search for innovative methods to distribute NASA's information lead a gross-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the services over the initial 6-month period. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained will allow NASA to ensure that its institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

Aho-Corasick String Matching on Shared and Distributed Memory Parallel Architectures

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

Tumeo, Antonino; Villa, Oreste; Chavarría-Miranda, Daniel

String matching is at the core of many critical applications, including network intrusion detection systems, search engines, virus scanners, spam filters, DNA and protein sequencing, and data mining. For all of these applications string matching requires a combination of (sometimes all) the following characteristics: high and/or predictable performance, support for large data sets and flexibility of integration and customization. Many software based implementations targeting conventional cache-based microprocessors fail to achieve high and predictable performance requirements, while Field-Programmable Gate Array (FPGA) implementations and dedicated hardware solutions fail to support large data sets (dictionary sizes) and are difficult to integrate and customize.more » The advent of multicore, multithreaded, and GPU-based systems is opening the possibility for software based solutions to reach very high performance at a sustained rate. This paper compares several software-based implementations of the Aho-Corasick string searching algorithm for high performance systems. We discuss the implementation of the algorithm on several types of shared-memory high-performance architectures (Niagara 2, large x86 SMPs and Cray XMT), distributed memory with homogeneous processing elements (InfiniBand cluster of x86 multicores) and heterogeneous processing elements (InfiniBand cluster of x86 multicores with NVIDIA Tesla C10 GPUs). We describe in detail how each solution achieves the objectives of supporting large dictionaries, sustaining high performance, and enabling customization and flexibility using various data sets.« less

Software for Information Storage and Retrieval Tested, Evaluated and Compared: Part VI--Various Additional Programs.

ERIC Educational Resources Information Center

Sieverts, Eric G.; And Others

1993-01-01

Reports on tests evaluating nine microcomputer software packages designed for information storage and retrieval: BRS-Search, dtSearch, InfoBank, Micro-OPC, Q&A, STN-PFS, Strix, TINman, and ZYindex. Tables and narrative evaluations detail results related to security, hardware, user features, search capability, indexing, input, maintenance of files,…

Visualization of Pulsar Search Data

NASA Astrophysics Data System (ADS)

Foster, R. S.; Wolszczan, A.

1993-05-01

The search for periodic signals from rotating neutron stars or pulsars has been a computationally taxing problem to astronomers for more than twenty-five years. Over this time interval, increases in computational capability have allowed ever more sensitive searches, covering a larger parameter space. The volume of input data and the general presence of radio frequency interference typically produce numerous spurious signals. Visualization of the search output and enhanced real-time processing of significant candidate events allow the pulsar searcher to optimally processes and search for new radio pulsars. The pulsar search algorithm and visualization system presented in this paper currently runs on serial RISC based workstations, a traditional vector based super computer, and a massively parallel computer. A description of the serial software algorithm and its modifications for massively parallel computing are describe. The results of four successive searches for millisecond period radio pulsars using the Arecibo telescope at 430 MHz have resulted in the successful detection of new long-period and millisecond period radio pulsars.

Data Telemetry and Acquisition System for Acoustic Signal Processing Investigations.

DTIC Science & Technology

1996-02-20

were VME- based computer systems operating under the VxWorks real - time operating system . Each system shared a common hardware and software... real - time operating system . It interfaces to the Berg PCM Decommutator board, which searches for the embedded synchronization word in the data and re...software were built on top of this architecture. The multi-tasking, message queue and memory management facilities of the VxWorks real - time operating system are

Sequence tagging reveals unexpected modifications in toxicoproteomics

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

2010-01-01

Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

A real-time KLT implementation for radio-SETI applications

NASA Astrophysics Data System (ADS)

Melis, Andrea; Concu, Raimondo; Pari, Pierpaolo; Maccone, Claudio; Montebugnoli, Stelio; Possenti, Andrea; Valente, Giuseppe; Antonietti, Nicoló; Perrodin, Delphine; Migoni, Carlo; Murgia, Matteo; Trois, Alessio; Barbaro, Massimo; Bocchinu, Alessandro; Casu, Silvia; Lunesu, Maria Ilaria; Monari, Jader; Navarrini, Alessandro; Pisanu, Tonino; Schilliró, Francesco; Vacca, Valentina

2016-07-01

SETI, the Search for ExtraTerrestrial Intelligence, is the search for radio signals emitted by alien civilizations living in the Galaxy. Narrow-band FFT-based approaches have been preferred in SETI, since their computation time only grows like N*lnN, where N is the number of time samples. On the contrary, a wide-band approach based on the Kahrunen-Lo`eve Transform (KLT) algorithm would be preferable, but it would scale like N*N. In this paper, we describe a hardware-software infrastructure based on FPGA boards and GPU-based PCs that circumvents this computation-time problem allowing for a real-time KLT.

Cloud4Psi: cloud computing for 3D protein structure similarity searching.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-10-01

Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

Cloud4Psi: cloud computing for 3D protein structure similarity searching

PubMed Central

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-01-01

Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. Contact: dariusz.mrozek@polsl.pl PMID:24930141

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

Software Assessment of the Global Force Management (GFM) Search Capability Study

DTIC Science & Technology

2017-02-01

Study by Timothy Hanratty, Mark Mittrick, Alex Vertlieb, and Frederick Brundick Approved for public release; distribution...Army Research Laboratory Software Assessment of the Global Force Management (GFM) Search Capability Study by Timothy Hanratty, Mark Mittrick...Force Management (GFM) Search Capability Study 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Timothy

Googling DNA sequences on the World Wide Web.

PubMed

Hajibabaei, Mehrdad; Singer, Gregory A C

2009-11-10

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Earth Orientation - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You are here: Home › USNO › Earth Orientation USNO Logo USNO Navigation Earth Orientation Products GPS -based Products VLBI-based Products EO Information Center Publications about Products Software Info Earth

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements

PubMed Central

Anada, Masato; Nakanishi-Ohno, Yoshinori; Okada, Masato; Kimura, Tsuyoshi; Wakabayashi, Yusuke

2017-01-01

Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes’ theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites. PMID:29217989

AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

PubMed Central

Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

2015-01-01

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com. PMID:20482635

CubeIndexer: Indexer for regions of interest in data cubes

NASA Astrophysics Data System (ADS)

Chilean Virtual Observatory; Araya, Mauricio; Candia, Gabriel; Gregorio, Rodrigo; Mendoza, Marcelo; Solar, Mauricio

2015-12-01

CubeIndexer indexes regions of interest (ROIs) in data cubes reducing the necessary storage space. The software can process data cubes containing megabytes of data in fractions of a second without human supervision, thus allowing it to be incorporated into a production line for displaying objects in a virtual observatory. The software forms part of the Chilean Virtual Observatory (ChiVO) and provides the capability of content-based searches on data cubes to the astronomical community.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined.

PubMed

Falkner, Jayson; Andrews, Philip

2005-05-15

Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. This problem deserves attention as new mass spectrometers provide the ability for higher throughput and as known protein datasets rapidly grow in size. New software algorithms need to be devised in order to address the performance issues of conventional MSMS protein dataset-based protein identification. This paper describes a novel algorithm based on converting a collection of monoisotopic, centroided spectra to a new data structure, named 'peptide finite state machine' (PFSM), which may be used to rapidly search a known dataset of protein sequences, regardless of the number of spectra searched or the number of potential modifications examined. The algorithm is verified using a set of commercially available tryptic digest protein standards analyzed using an ABI 4700 MALDI TOFTOF mass spectrometer, and a free, open source PFSM implementation. It is illustrated that a PFSM can accurately search large collections of spectra against large datasets of protein sequences (e.g. NCBI nr) using a regular desktop PC; however, this paper only details the method for identifying peptide and subsequently protein candidates from a dataset of known protein sequences. The concept of using a PFSM as a peptide pre-screening technique for MSMS-based search engines is validated by using PFSM with Mascot and XTandem. Complete source code, documentation and examples for the reference PFSM implementation are freely available at the Proteome Commons, http://www.proteomecommons.org and source code may be used both commercially and non-commercially as long as the original authors are credited for their work.

ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite

PubMed Central

2010-01-01

Background Successful application of crosslinking combined with mass spectrometry for studying proteins and protein complexes requires specifically-designed crosslinking reagents, experimental techniques, and data analysis software. Using isotopically-coded ("heavy and light") versions of the crosslinker and cleavable crosslinking reagents is analytically advantageous for mass spectrometric applications and provides a "handle" that can be used to distinguish crosslinked peptides of different types, and to increase the confidence of the identification of the crosslinks. Results Here, we describe a program suite designed for the analysis of mass spectrometric data obtained with isotopically-coded cleavable crosslinkers. The suite contains three programs called: DX, DXDX, and DXMSMS. DX searches the mass spectra for the presence of ion signal doublets resulting from the light and heavy isotopic forms of the isotopically-coded crosslinking reagent used. DXDX searches for possible mass matches between cleaved and uncleaved isotopically-coded crosslinks based on the established chemistry of the cleavage reaction for a given crosslinking reagent. DXMSMS assigns the crosslinks to the known protein sequences, based on the isotopically-coded and un-coded MS/MS fragmentation data of uncleaved and cleaved peptide crosslinks. Conclusion The combination of these three programs, which are tailored to the analytical features of the specific isotopically-coded cleavable crosslinking reagents used, represents a powerful software tool for automated high-accuracy peptide crosslink identification. See: http://www.creativemolecules.com/CM_Software.htm PMID:20109223

The use of Research Electronic Data Capture (REDCap) software to create a database of librarian-mediated literature searches.

PubMed

Lyon, Jennifer A; Garcia-Milian, Rolando; Norton, Hannah F; Tennant, Michele R

2014-01-01

Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This article describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users' needs, tracking librarian effort, and focusing librarians' continuing education.

Frequency Estimator Performance for a Software-Based Beacon Receiver

NASA Technical Reports Server (NTRS)

Zemba, Michael J.; Morse, Jacquelynne R.; Nessel, James A.

2014-01-01

As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a Q/V-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

Digital Equipment Corporation's CRDOM Software and Database Publications.

ERIC Educational Resources Information Center

Adams, Michael Q.

1986-01-01

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Transaction Logging.

ERIC Educational Resources Information Center

Jones, S.; And Others

1997-01-01

Discusses the use of transaction logging in Okapi-related projects to allow search algorithms and user interfaces to be investigated, evaluated, and compared. A series of examples is presented, illustrating logging software for character-based and graphical user interface systems, and demonstrating the usefulness of relational database management…

Telecommunications and data acquisition

NASA Technical Reports Server (NTRS)

Renzetti, N. A. (Editor)

1981-01-01

Deep Space Network progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations is reported. In addition, developments in Earth based radio technology as applied to geodynamics, astrophysics, and the radio search for extraterrestrial intelligence are reported.

Science Software in High-Button Shoes.

ERIC Educational Resources Information Center

Dyrli, Odvard Egil

1984-01-01

Discusses inquiry-oriented science instruction and experientially based programs that support newer instructional strategies. Also provides examples of six process-oriented programs (Cat Lab, Geology Search, Rocky's Boots, Tell Star, Volcanoes, What's in Your Lunch?). Level, hardware needed, publisher, and description are provided for each…

ISE: An Integrated Search Environment. The manual

NASA Technical Reports Server (NTRS)

Chu, Lon-Chan

1992-01-01

Integrated Search Environment (ISE), a software package that implements hierarchical searches with meta-control, is described in this manual. ISE is a collection of problem-independent routines to support solving searches. Mainly, these routines are core routines for solving a search problem and they handle the control of searches and maintain the statistics related to searches. By separating the problem-dependent and problem-independent components in ISE, new search methods based on a combination of existing methods can be developed by coding a single master control program. Further, new applications solved by searches can be developed by coding the problem-dependent parts and reusing the problem-independent parts already developed. Potential users of ISE are designers of new application solvers and new search algorithms, and users of experimental application solvers and search algorithms. The ISE is designed to be user-friendly and information rich. In this manual, the organization of ISE is described and several experiments carried out on ISE are also described.

Monkey search algorithm for ECE components partitioning

NASA Astrophysics Data System (ADS)

Kuliev, Elmar; Kureichik, Vladimir; Kureichik, Vladimir, Jr.

2018-05-01

The paper considers one of the important design problems – a partitioning of electronic computer equipment (ECE) components (blocks). It belongs to the NP-hard class of problems and has a combinatorial and logic nature. In the paper, a partitioning problem formulation can be found as a partition of graph into parts. To solve the given problem, the authors suggest using a bioinspired approach based on a monkey search algorithm. Based on the developed software, computational experiments were carried out that show the algorithm efficiency, as well as its recommended settings for obtaining more effective solutions in comparison with a genetic algorithm.

Novel technology as platform for interventions for caregivers and individuals with severe mental health illnesses: A systematic review.

PubMed

Meyer, Thomas D; Casarez, Rebecca; Mohite, Satyajit S; La Rosa, Nikki; Iyengar, M Sriram

2018-01-15

Severe mental illnesses (SMIs) have been found to be associated with both increases in morbidity-mortality, need for treatment care in patients themselves, and burden for relatives as caregivers. A growing number of web-based and mobile software applications have appeared that aim to address various barriers with respect to access to care. Our objective was to review and summarize recent advancements in such interventions for caregivers of individuals with a SMI. We conducted a systematic search for papers evaluating interactive mobile or web-based software (using no or only minimal support from a professional) specifically aimed at supporting informal caregivers. We also searched for those supporting patients with SMI so as to not to miss any which might include relatives. Out of a total of 1673 initial hits, we identified 11 articles reporting on 9 different mobile or web-based software programs. The main result is that none of those studies focused on caregivers, and the ones we identified using mobile or web-based applications were just for patients and not their relatives. Differentiating between online and offline available software might not always have been totally reliable, and we might have therefore missed some studies. In summary, the studies provided evidence that remotely accessible interventions for patients with SMI are feasible and acceptable to patients. No such empirically evaluated program was available for informal caregivers such as relatives. Keeping in mind the influential role of those informal caregivers in the process of treatment and self-management, this is highly relevant for public health. Supporting informal caregivers can improve well-being of both caregivers and patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Capi text V.1--data analysis software for nailfold skin capillaroscopy.

PubMed

Dobrev, Hristo P

2007-01-01

Nailfold skin capillaroscopy is a simple non-invasive method used to assess conditions of disturbed microcirculation such as Raynaud's phenomenon, acrocyanosis, perniones, connective tissue diseases, psoriasis, diabetes mellitus, neuropathy and vibration disease. To develop data analysis software aimed at assisting the documentation and analysis of a capillaroscopic investigation. SOFTWARE DESCRIPTION: The programme is based on a modular principle. The module "Nomenclatures" includes menus for the patients' data. The module "Examinations" includes menus for all general and specific aspects of the medical examination and capillaroscopic investigations. The modules "Settings" and "Information" include customization menus for the programme. The results of nailfold capillaroscopy can be printed in a short or expanded form. This software allows physicians to perform quick search by using various specified criteria and prepare analyses and reports. This software programme will facilitate any practitioner who performs nailfold skin capillaroscopy.

The telecommunications and data acquisition report

NASA Technical Reports Server (NTRS)

Renzetti, N. A.

1980-01-01

Deep Space Network progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implemention, and operations is documented. In addition, developments in Earth based radio technology as applied to geodynamics, astrophysics, and the radio search for extraterrestrial intelligence are reported.

The Telecommunications and Data Acquisition Report

NASA Technical Reports Server (NTRS)

Posner, E. C. (Editor)

1986-01-01

Deep Space Network progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations is documented. In addition, developments in Earth-based radio technology as applied to geodynamics, astrophysics and the radio search for extraterrestrial intelligence are reported.

Calyx{trademark} EA implementation at AECB

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

NONE

1997-12-31

This report describes a project to examine the applicability of a knowledge-based decision support software for environmental assessment (Calyx) to assist the Atomic Energy Control Board in environmental screenings, assessment, management, and database searches. The report begins with background on the Calyx software and then reviews activities with regard to modification of the Calyx knowledge base for application to the nuclear sector. This is followed by lists of standard activities handled by the software and activities specific to the Board; the hierarchy of environmental components developed for the Board; details of impact rules that describe the conditions under which environmentalmore » impacts will occur (the bulk of the report); information on mitigation and monitoring rules and on instance data; and considerations for future work on implementing Calyx at the Board. Appendices include an introduction to expert systems and an overview of the Calyx knowledge base structure.« less

TMS for Instantiating a Knowledge Base With Incomplete Data

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

A computer program that belongs to the class known among software experts as output truth-maintenance-systems (output TMSs) has been devised as one of a number of software tools for reducing the size of the knowledge base that must be searched during execution of artificial- intelligence software of the rule-based inference-engine type in a case in which data are missing. This program determines whether the consequences of activation of two or more rules can be combined without causing a logical inconsistency. For example, in a case involving hypothetical scenarios that could lead to turning a given device on or off, the program determines whether a scenario involving a given combination of rules could lead to turning the device both on and off at the same time, in which case that combination of rules would not be included in the scenario.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

PubMed

Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

2017-09-13

Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

End-user searching: impetus for an expanding information management and technology role for the hospital librarian.

PubMed Central

Klein, M S; Ross, F

1997-01-01

Using the results of the 1993 Medical Library Association (MLA) Hospital Libraries Section survey of hospital-based end-user search services, this article describes how end-user search services can become an impetus for an expanded information management and technology role for the hospital librarian. An end-user services implementation plan is presented that focuses on software, hardware, finances, policies, staff allocations and responsibilities, educational program design, and program evaluation. Possibilities for extending end-user search services into information technology and informatics, specialized end-user search systems, and Internet access are described. Future opportunities are identified for expanding the hospital librarian's role in the face of changing health care management, advances in information technology, and increasing end-user expectations. PMID:9285126

Agreement between Medline searches using the Medline-CD-Rom and Internet Pubmed, BioMedNet, Medscape and Gateway search-engines.

PubMed

Caro-Rojas, Rosa Angela; Eslava-Schmalbach, Javier H

2005-01-01

To compare the information obtained from the Medline database using Internet commercial search engines with that obtained from a compact disc (Medline-CD). An agreement study was carried out based on 101 clinical scenarios provided by specialists in internal medicine, pharmacy, gynaecology-obstetrics, surgery and paediatrics. 175 search strategies were employed using the connector AND plus text within quotation marks. The search was limited to 1991-1999. Internet search-engines were selected by common criteria. Identical search strategies were independently applied to and masked from Internet search engines, as well as the Medline-CD. 3,488 articles were obtained using 129 search strategies. Agreement with the Medline-CD was 54% for PubMed, 57% for Gateway, 54% for Medscape and 65% for BioMedNet. The highest agreement rate for a given speciality (paediatrics) was 78.1% for BioMedNet, having greater -/- than +/+ agreement. Even though free access to Medline has encouraged the boom and growth of evidence-based medicine, these results must be considered within the context of which search engine was selected for doing the searches. The Internet search engines studied showed a poor agreement with the Medline-CD, the rate of agreement differing according to speciality, thus significantly affecting searches and their reproducibility. Software designed for conducting Medline database searches, including the Medline-CD, must be standardised and validated.

The JPL Library information retrieval system

NASA Technical Reports Server (NTRS)

Walsh, J.

1975-01-01

The development, capabilities, and products of the computer-based retrieval system of the Jet Propulsion Laboratory Library are described. The system handles books and documents, produces a book catalog, and provides a machine search capability. Programs and documentation are available to the public through NASA's computer software dissemination program.

The Telecommunications and Data Acquisition Report

NASA Technical Reports Server (NTRS)

Posner, E. C. (Editor)

1985-01-01

Deep Space Network (DSN) progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operation is discussed. In addition, developments in Earth-based radio technology as applied to geodynamics, astrophysics and the radio search for extraterrestrial intelligence are reported.

The search for extrasolar planets: Study of line bisectors and its relation with precise radial velocity measurements

NASA Astrophysics Data System (ADS)

Martinez Fiorenzano, A. F.

2006-03-01

(Abridged) To this purpose, in the course of the thesis work we prepared a suitable software in order to use the same spectra acquired for radial velocity determinations (i.e., with the spectrum of the Iodine cell imprinted on) to measure variations of the stellar line profiles. This is a novel approach, that can be of general utility in all high precision radial velocity surveys based on iodine cell data. This software has then been extensively used on data acquired within our survey, allowing a proper insight into a number of interesting cases, where spurious estimates of the radial velocities due to activity or contamination by light from the companions were revealed. The same technique can also be considered to correct the measured radial velocities, in order to search for planets around active stars.

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

FloPSy - Search-Based Floating Point Constraint Solving for Symbolic Execution

NASA Astrophysics Data System (ADS)

Lakhotia, Kiran; Tillmann, Nikolai; Harman, Mark; de Halleux, Jonathan

Recently there has been an upsurge of interest in both, Search-Based Software Testing (SBST), and Dynamic Symbolic Execution (DSE). Each of these two approaches has complementary strengths and weaknesses, making it a natural choice to explore the degree to which the strengths of one can be exploited to offset the weakness of the other. This paper introduces an augmented version of DSE that uses a SBST-based approach to handling floating point computations, which are known to be problematic for vanilla DSE. The approach has been implemented as a plug in for the Microsoft Pex DSE testing tool. The paper presents results from both, standard evaluation benchmarks, and two open source programs.

Dataflow Design Tool: User's Manual

NASA Technical Reports Server (NTRS)

Jones, Robert L., III

1996-01-01

The Dataflow Design Tool is a software tool for selecting a multiprocessor scheduling solution for a class of computational problems. The problems of interest are those that can be described with a dataflow graph and are intended to be executed repetitively on a set of identical processors. Typical applications include signal processing and control law problems. The software tool implements graph-search algorithms and analysis techniques based on the dataflow paradigm. Dataflow analyses provided by the software are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool provides performance optimization through the inclusion of artificial precedence constraints among the schedulable tasks. The user interface and tool capabilities are described. Examples are provided to demonstrate the analysis, scheduling, and optimization functions facilitated by the tool.

Mail LOG: Program operating instructions

NASA Technical Reports Server (NTRS)

Harris, D. K.

1979-01-01

The operating instructions for the software package, MAIL LOG, developed for the Scout Project Automatic Data System, SPADS, are provided. The program is written in FORTRAN for the PRIME 300 computer system. The MAIL LOG program has the following four modes of operation: (1) INPUT - putting new records into the data base (2) REVISE - changing or modifying existing records in the data base (3) SEARCH - finding special records existing in the data base (4) ARCHIVE - store or put away existing records in the data base. The output includes special printouts of records in the data base and results from the INPUT and SEARCH modes. The MAIL LOG data base consists of three main subfiles: Incoming and outgoing mail correspondence; Design Information Releases and Releases and Reports; and Drawings and Engineering orders.

After Losing Users in Catalogs, Libraries Find Better Search Software

ERIC Educational Resources Information Center

Parry, Marc

2010-01-01

Traditional online library catalogs do not tend to order search results by ranked relevance, and they can befuddle users with clunky interfaces. However, that's changing because of two technology trends. First, a growing number of universities are shelling out serious money for sophisticated software that makes exploring their collections more…

Computer Software for Forestry Technology Curricula. Final Report.

ERIC Educational Resources Information Center

Watson, Roy C.; Scobie, Walter R.

Since microcomputers are being used more and more frequently in the forest products industry in the Pacific Northwest, Green River Community College conducted a project to search for BASIC language computer programs pertaining to forestry, and when possible, to adapt such software for use in teaching forestry technology. The search for applicable…

Search and retrieval of office files using dBASE 3

NASA Technical Reports Server (NTRS)

Breazeale, W. L.; Talley, C. R.

1986-01-01

Described is a method of automating the office files retrieval process using a commercially available software package (dBASE III). The resulting product is a menu-driven computer program which requires no computer skills to operate. One part of the document is written for the potential user who has minimal computer experience and uses sample menu screens to explain the program; while a second part is oriented towards the computer literate individual and includes rather detailed descriptions of the methodology and search routines. Although much of the programming techniques are explained, this document is not intended to be a tutorial on dBASE III. It is hoped that the document will serve as a stimulus for other applications of dBASE III.

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

PubMed Central

2013-01-01

Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator. PMID:23865810

Knowledge-based reusable software synthesis system

NASA Technical Reports Server (NTRS)

Donaldson, Cammie

1989-01-01

The Eli system, a knowledge-based reusable software synthesis system, is being developed for NASA Langley under a Phase 2 SBIR contract. Named after Eli Whitney, the inventor of interchangeable parts, Eli assists engineers of large-scale software systems in reusing components while they are composing their software specifications or designs. Eli will identify reuse potential, search for components, select component variants, and synthesize components into the developer's specifications. The Eli project began as a Phase 1 SBIR to define a reusable software synthesis methodology that integrates reusabilityinto the top-down development process and to develop an approach for an expert system to promote and accomplish reuse. The objectives of the Eli Phase 2 work are to integrate advanced technologies to automate the development of reusable components within the context of large system developments, to integrate with user development methodologies without significant changes in method or learning of special languages, and to make reuse the easiest operation to perform. Eli will try to address a number of reuse problems including developing software with reusable components, managing reusable components, identifying reusable components, and transitioning reuse technology. Eli is both a library facility for classifying, storing, and retrieving reusable components and a design environment that emphasizes, encourages, and supports reuse.

Collecting and Using Networked Statistics: Current Status, Future Goals

ERIC Educational Resources Information Center

Hiott, Judith

2004-01-01

For more than five years the Houston Public Library has collected statistics for measuring networked collections and services based on emerging guidelines. While the guidelines have provided authority and stability to the process, the clarification process continues. The development of information discovery software, such as federated search tools…

Fast radio burst search: cross spectrum vs. auto spectrum method

NASA Astrophysics Data System (ADS)

Liu, Lei; Zheng, Weimin; Yan, Zhen; Zhang, Juan

2018-06-01

The search for fast radio bursts (FRBs) is a hot topic in current radio astronomy studies. In this work, we carry out a single pulse search with a very long baseline interferometry (VLBI) pulsar observation data set using both auto spectrum and cross spectrum search methods. The cross spectrum method, first proposed in Liu et al., maximizes the signal power by fully utilizing the fringe phase information of the baseline cross spectrum. The auto spectrum search method is based on the popular pulsar software package PRESTO, which extracts single pulses from the auto spectrum of each station. According to our comparison, the cross spectrum method is able to enhance the signal power and therefore extract single pulses from data contaminated by high levels of radio frequency interference (RFI), which makes it possible to carry out a search for FRBs in regular VLBI observations when RFI is present.

DOIDB: Reusing DataCite's search software as metadata portal for GFZ Data Services

NASA Astrophysics Data System (ADS)

Elger, K.; Ulbricht, D.; Bertelmann, R.

2016-12-01

GFZ Data Services is the central service point for the publication of research data at the Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences (GFZ). It provides data publishing services to scientists of GFZ, associated projects, and associated institutions. The publishing services aim to make research data and physical samples visible and citable, by assigning persistent identifiers (DOI, IGSN) and by complementing existing IT infrastructure. To integrate several research domains a modular software stack that is made of free software components has been created to manage data and metadata as well as register persistent identifiers [1]. Pivotal component for the registration of DOIs is the DOIDB. It has been derived from three software components provided by DataCite [2] that moderate the registration of DOIs and the deposition of metadata, allow the dissemination of metadata, and provide a user interface to navigate and discover datasets. The DOIDB acts as a proxy to the DataCite infrastructure and in addition to the DataCite metadata schema, it allows to deposit and disseminate metadata following the schemas ISO19139 and NASA GCMD DIF. The search component has been modified to meet the requirements of a geosciences metadata portal. In particular, the search component has been altered to make use of Apache SOLRs capability to index and query spatial coordinates. Furthermore, the user interface has been adjusted to provide a first impression of the data by showing a map, summary information and subjects. DOIDB and its components are available on GitHub [3].We present a software solution for registration of DOIs that allows to integrate existing data systems, keeps track of registered DOIs, and provides a metadata portal to discover datasets [4]. [1] Ulbricht, D.; Elger, K.; Bertelmann, R.; Klump, J. panMetaDocs, eSciDoc, and DOIDB—An Infrastructure for the Curation and Publication of File-Based Datasets for GFZ Data Services. ISPRS Int. J. Geo-Inf. 2016, 5, 25. http://doi.org/10.3390/ijgi5030025[2] https://github.com/datacite[3] https://github.com/ulbricht/search/tree/doidb , https://github.com/ulbricht/mds/tree/doidb , https://github.com/ulbricht/oaip/tree/doidb[4] http://doidb.wdc-terra.org

Input-independent, Scalable and Fast String Matching on the Cray XMT

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

Villa, Oreste; Chavarría-Miranda, Daniel; Maschhoff, Kristyn J

2009-05-25

String searching is at the core of many security and network applications like search engines, intrusion detection systems, virus scanners and spam filters. The growing size of on-line content and the increasing wire speeds push the need for fast, and often real- time, string searching solutions. For these conditions, many software implementations (if not all) targeting conventional cache-based microprocessors do not perform well. They either exhibit overall low performance or exhibit highly variable performance depending on the types of inputs. For this reason, real-time state of the art solutions rely on the use of either custom hardware or Field-Programmable Gatemore » Arrays (FPGAs) at the expense of overall system flexibility and programmability. This paper presents a software based implementation of the Aho-Corasick string searching algorithm on the Cray XMT multithreaded shared memory machine. Our so- lution relies on the particular features of the XMT architecture and on several algorith- mic strategies: it is fast, scalable and its performance is virtually content-independent. On a 128-processor Cray XMT, it reaches a scanning speed of ≈ 28 Gbps with a performance variability below 10 %. In the 10 Gbps performance range, variability is below 2.5%. By comparison, an Intel dual-socket, 8-core system running at 2.66 GHz achieves a peak performance which varies from 500 Mbps to 10 Gbps depending on the type of input and dictionary size.« less

An integrated software suite for surface-based analyses of cerebral cortex.

PubMed

Van Essen, D C; Drury, H A; Dickson, J; Harwell, J; Hanlon, D; Anderson, C H

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.

An integrated software suite for surface-based analyses of cerebral cortex

NASA Technical Reports Server (NTRS)

Van Essen, D. C.; Drury, H. A.; Dickson, J.; Harwell, J.; Hanlon, D.; Anderson, C. H.

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.

The use of a genetic algorithm-based search strategy in geostatistics: application to a set of anisotropic piezometric head data

NASA Astrophysics Data System (ADS)

Abedini, M. J.; Nasseri, M.; Burn, D. H.

2012-04-01

In any geostatistical study, an important consideration is the choice of an appropriate, repeatable, and objective search strategy that controls the nearby samples to be included in the location-specific estimation procedure. Almost all geostatistical software available in the market puts the onus on the user to supply search strategy parameters in a heuristic manner. These parameters are solely controlled by geographical coordinates that are defined for the entire area under study, and the user has no guidance as to how to choose these parameters. The main thesis of the current study is that the selection of search strategy parameters has to be driven by data—both the spatial coordinates and the sample values—and cannot be chosen beforehand. For this purpose, a genetic-algorithm-based ordinary kriging with moving neighborhood technique is proposed. The search capability of a genetic algorithm is exploited to search the feature space for appropriate, either local or global, search strategy parameters. Radius of circle/sphere and/or radii of standard or rotated ellipse/ellipsoid are considered as the decision variables to be optimized by GA. The superiority of GA-based ordinary kriging is demonstrated through application to the Wolfcamp Aquifer piezometric head data. Assessment of numerical results showed that definition of search strategy parameters based on both geographical coordinates and sample values improves cross-validation statistics when compared with that based on geographical coordinates alone. In the case of a variable search neighborhood for each estimation point, optimization of local search strategy parameters for an elliptical support domain—the orientation of which is dictated by anisotropic axes—via GA was able to capture the dynamics of piezometric head in west Texas/New Mexico in an efficient way.

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.

PubMed

He, Ji; Dai, Xinbin; Zhao, Xuechun

2007-02-09

BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at http://bioinfo.noble.org/plan/. The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users.

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

PubMed Central

He, Ji; Dai, Xinbin; Zhao, Xuechun

2007-01-01

Background BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. Results Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. Conclusion PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at . The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users. PMID:17291345

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets

PubMed Central

Johnson, Z. P.; Eady, R. D.; Ahmad, S. F.; Agravat, S.; Morris, T; Else, J; Lank, S. M.; Wiseman, R. W.; O’Connor, D. H.; Penedo, M. C. T.; Larsen, C. P.

2012-01-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permitsmultiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox onWindows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie. kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo, user name: imsdemo7@gmail.com and password: imsdemo. PMID:22080300

Immunogenetic Management Software: a new tool for visualization and analysis of complex immunogenetic datasets.

PubMed

Johnson, Z P; Eady, R D; Ahmad, S F; Agravat, S; Morris, T; Else, J; Lank, S M; Wiseman, R W; O'Connor, D H; Penedo, M C T; Larsen, C P; Kean, L S

2012-04-01

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Captivating Open University Students with Online Literature Search Tutorials Created Using Screen Capture Software

ERIC Educational Resources Information Center

Wales, Tim; Robertson, Penny

2008-01-01

Purpose: The aim of this paper is to share the experiences and challenges faced by the Open University Library (OUL) in using screen capture software to develop online literature search tutorials. Design/methodology/approach: A summary of information literacy support at the OUL is provided as background information to explain the decision to…

Information Technology and the Evolution of the Library

DTIC Science & Technology

2009-03-01

Resource Commons/ Repository/ Federated Search ILS (GLADIS/Pathfinder - Millenium)/ Catalog/ Circulation/ Acquisitions/ Digital Object Content...content management services to help centralize and distribute digi- tal content from across the institution, software to allow for seamless federated ... search - ing across multiple databases, and imaging software to allow for daily reimaging of ter- minals to reduce security concerns that otherwise

How To Use the SilverPlatter Software To Search the ERIC CD ROM.

ERIC Educational Resources Information Center

Merrill, Paul F.

This manual provides detailed instructions for using SilverPlatter software to search the ERIC CD ROM (Compact Disk Read Only Memory), a large bibliographic database relating to education which contains reference information on numerous journal articles from over 750 journals cited in the "Current Index to Journals in Education" (CIJE),…

HBVPathDB: a database of HBV infection-related molecular interaction network.

PubMed

Zhang, Yi; Bo, Xiao-Chen; Yang, Jing; Wang, Sheng-Qi

2005-03-21

To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data.

PubMed

Lommen, Arjen; van der Kamp, Henk J; Kools, Harrie J; van der Lee, Martijn K; van der Weg, Guido; Mol, Hans G J

2012-11-09

A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has been developed for and tested on LECO data. The software is developed to run multi-threaded (one thread per processor core) on a standard PC (personal computer) under different operating systems and is as such capable of processing multiple data sets simultaneously. Raw data files are converted into netCDF (network Common Data Form) format using a fast conversion tool. They are then preprocessed using previously developed algorithms originating from metAlign software. Next, the resulting reduced data files are searched against a user-composed library (derived from user or commercial NIST-compatible libraries) (NIST=National Institute of Standards and Technology) and the identified compounds, including an indicative concentration, are reported in Excel format. Data can be processed batch wise. The overall time needed for conversion together with processing and searching of 30 raw data sets for 560 compounds is routinely within an hour. The screening performance is evaluated for detection of pesticides and contaminants in raw data obtained after analysis of soil and plant samples. Results are compared to the existing data-handling routine based on proprietary software (LECO, ChromaTOF). The developed software tool set, which is freely downloadable at www.metalign.nl, greatly accelerates data-analysis and offers more options for fine-tuning automated identification toward specific application needs. The quality of the results obtained is slightly better than the standard processing and also adds a quantitative estimate. The software tool set in combination with two-dimensional gas chromatography coupled to time-of-flight mass spectrometry shows great potential as a highly-automated and fast multi-residue instrumental screening method. Copyright © 2012 Elsevier B.V. All rights reserved.

The Weapons Laboratory Technical Library: Automating with ’Stilas’

DTIC Science & Technology

1990-03-01

version of the system to LC in October 1988. -X- A small business specializing in library automation, SIRSI was founded in 1979 by library and...computer specialists, and has a strong reputation based upon the success of their UNIX-based Unicorn Collection Management System. SIRSI offers a complete...system based on the Unicorn and BRS/ Search systems. The contracted STILAS package includes UNISYS hardware, software written in the C language

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

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

Bosler, Peter

Stride Search provides a flexible tool for detecting storms or other extreme climate events in high-resolution climate data sets saved on uniform latitude-longitude grids in standard NetCDF format. Users provide the software a quantitative description of a meteorological event they are interested in; the software searches a data set for locations in space and time that meet the user’s description. In its first stage, Stride Search performs a spatial search of the data set at each timestep by dividing a search domain into circular sectors of constant geodesic radius. Data from a netCDF file is read into memory for eachmore » circular search sector. If the data meet or exceed a set of storm identification criteria (defined by the user), a storm is recorded to a linked list. Finally, the linked list is examined and duplicate detections of the same storm are removed and the results are written to an output file. The first stage’s output file is read by a second program that builds storm. Additional identification criteria may be applied at this stage to further classify storms. Storm tracks are the software’s ultimate output and routines are provided for formatting that output for various external software libraries for plotting and tabulating data.« less

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Problem-solving skills in high school biology: The effectiveness of the IMMEX problem-solving assessment software

NASA Astrophysics Data System (ADS)

Palacio-Cayetano, Joycelin

"Problem-solving through reflective thinking should be both the method and valuable outcome of science instruction in America's schools" proclaimed John Dewey (Gabel, 1995). If the development of problem-solving is a primary goal of science education, more problem-solving opportunities must be an integral part of K-16 education. To examine the effective use of technology in developing and assessing problem-solving skills, a problem-solving authoring, learning, and assessment software, the UCLA IMMEX Program-Interactive Multimedia Exercises-was investigated. This study was a twenty-week quasi-experimental study that was implemented as a control-group time series design among 120 tenth grade students. Both the experimental group (n = 60) and the control group (n = 60) participated in a problem-based learning curriculum; however, the experimental group received regular intensive experiences with IMMEX problem-solving and the control group did not. Problem-solving pretest and posttest were administered to all students. The instruments used were a 35-item Processes of Biological Inquiry Test and an IMMEX problem-solving assessment test, True Roots. Students who participated in the IMMEX Program achieved significant (p <.05) gains in problem-solving skills on both problem-solving assessment instruments. This study provided evidence that IMMEX software is highly efficient in evaluating salient elements of problem-solving. Outputs of students' problem-solving strategies revealed that unsuccessful problem solvers primarily used the following four strategies: (1) no data search strategy, students simply guessed; (2) limited data search strategy leading to insufficient data and premature closing; (3) irrelevant data search strategy, students focus in areas bearing no substantive data; and (4) extensive data search strategy with inadequate integration and analysis. On the contrary, successful problem solvers used the following strategies; (1) focused search strategy coupled with the ability to fill in knowledge gaps by accessing the appropriate resources; (2) targeted search strategy coupled with high level of analytical and integration skills; and (3) focused search strategy coupled with superior discrimination, analytical, and integration skills. The strategies of students who were successful and unsuccessful solving IMMEX problems were consistent with those of expert and novice problem solvers identified in the literature on problem-solving.

PolyPhred analysis software for mutation detection from fluorescence-based sequence data.

PubMed

Montgomery, Kate T; Iartchouck, Oleg; Li, Li; Loomis, Stephanie; Obourn, Vanessa; Kucherlapati, Raju

2008-10-01

The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect. The software is being continually updated to permit further automation of mutation analysis. Currently, however, at least some manual review is required if one wishes to identify 100% of the variants in a sample set.

A computing method for spatial accessibility based on grid partition

NASA Astrophysics Data System (ADS)

Ma, Linbing; Zhang, Xinchang

2007-06-01

An accessibility computing method and process based on grid partition was put forward in the paper. As two important factors impacting on traffic, density of road network and relative spatial resistance for difference land use was integrated into computing traffic cost in each grid. A* algorithms was inducted to searching optimum traffic cost of grids path, a detailed searching process and definition of heuristic evaluation function was described in the paper. Therefore, the method can be implemented more simply and its data source is obtained more easily. Moreover, by changing heuristic searching information, more reasonable computing result can be obtained. For confirming our research, a software package was developed with C# language under ArcEngine9 environment. Applying the computing method, a case study on accessibility of business districts in Guangzhou city was carried out.

Hybrid Differential Dynamic Programming with Stochastic Search

NASA Technical Reports Server (NTRS)

Aziz, Jonathan; Parker, Jeffrey; Englander, Jacob

2016-01-01

Differential dynamic programming (DDP) has been demonstrated as a viable approach to low-thrust trajectory optimization, namely with the recent success of NASAs Dawn mission. The Dawn trajectory was designed with the DDP-based Static Dynamic Optimal Control algorithm used in the Mystic software. Another recently developed method, Hybrid Differential Dynamic Programming (HDDP) is a variant of the standard DDP formulation that leverages both first-order and second-order state transition matrices in addition to nonlinear programming (NLP) techniques. Areas of improvement over standard DDP include constraint handling, convergence properties, continuous dynamics, and multi-phase capability. DDP is a gradient based method and will converge to a solution nearby an initial guess. In this study, monotonic basin hopping (MBH) is employed as a stochastic search method to overcome this limitation, by augmenting the HDDP algorithm for a wider search of the solution space.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

Genetic algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steven E.

1991-01-01

Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

Knowledge-based control of an adaptive interface

NASA Technical Reports Server (NTRS)

Lachman, Roy

1989-01-01

The analysis, development strategy, and preliminary design for an intelligent, adaptive interface is reported. The design philosophy couples knowledge-based system technology with standard human factors approaches to interface development for computer workstations. An expert system has been designed to drive the interface for application software. The intelligent interface will be linked to application packages, one at a time, that are planned for multiple-application workstations aboard Space Station Freedom. Current requirements call for most Space Station activities to be conducted at the workstation consoles. One set of activities will consist of standard data management services (DMS). DMS software includes text processing, spreadsheets, data base management, etc. Text processing was selected for the first intelligent interface prototype because text-processing software can be developed initially as fully functional but limited with a small set of commands. The program's complexity then can be increased incrementally. The intelligent interface includes the operator's behavior and three types of instructions to the underlying application software are included in the rule base. A conventional expert-system inference engine searches the data base for antecedents to rules and sends the consequents of fired rules as commands to the underlying software. Plans for putting the expert system on top of a second application, a database management system, will be carried out following behavioral research on the first application. The intelligent interface design is suitable for use with ground-based workstations now common in government, industrial, and educational organizations.

Using C to build a satellite scheduling expert system: Examples from the Explorer Platform planning system

NASA Technical Reports Server (NTRS)

Mclean, David R.; Tuchman, Alan; Potter, William J.

1991-01-01

A C-based artificial intelligence (AI) development effort which is based on a software tools approach is discussed with emphasis on reusability and maintainability of code. The discussion starts with simple examples of how list processing can easily be implemented in C and then proceeds to the implementations of frames and objects which use dynamic memory allocation. The implementation of procedures which use depth first search, constraint propagation, context switching, and blackboard-like simulation environment are described. Techniques for managing the complexity of C-based AI software are noted, especially the object-oriented techniques of data encapsulation and incremental development. Finally, all these concepts are put together by describing the components of planning software called the Planning And Resource Reasoning (PARR) Shell. This shell was successfully utilized for scheduling services of the Tracking and Data Relay Satellite System for the Earth Radiation Budget Satellite since May of 1987 and will be used for operations scheduling of the Explorer Platform in Nov. of 1991.

The NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Paulson, Sharon S.; Binkley, Robert L.; Kellogg, Yvonne D.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael J.; Accomazzi, Alberto

1995-01-01

The National Aeronautics and Space Act of 1958 established NASA and charged it to "provide for the widest practicable and appropriate dissemination of information concerning its activities and the results thereof." The search for innovative methods to distribute NASA's information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the service. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained ensures that NASA's institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

PubMed

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-11-27

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

PubMed Central

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-01-01

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

Use of notebook computers for third-year surgical students.

PubMed

Prystowsky, J B; Hassan, M B; Nahrwold, D L

1996-08-01

Computer-aided instruction has become increasingly popular in medical education. Notebook computers (NCs) are attractive, convenient microcomputers. We hypothesized that use of NCs by third-year surgical students would enhance their performance of educational activities. During the 1994-1995 academic year 25 student volunteers used NCs during the surgery clerkship. NC software included questions for self-examination, anatomy self-instruction program, word processing and electronic mail (e-mail) for recording and sending history and physicals (H & Ps) to faculty for review, and MEDLINE search software. Identical software was available to all students at on-campus computer centers. All students were asked to record the number of hours that they used the self-examination and anatomy programs, number of H & Ps performed and reviewed by faculty, and number of literature searches performed. NC users were interviewed regarding the value of NC use and their rating of software programs. NC users (n = 25) used the self-examination and anatomy programs more often, performed more literature searches, and had a greater percentage of their H & Ps reviewed by faculty compared with non-NC users (n = 143) (p < 0.05 for all outcomes). Most NC users agreed that NC use was enjoyable and valuable, and they believed that all students should have NCs during the surgery clerkship. Students rated software in order of preference: e-mail > self-examination > MEDLINE search > anatomy program. NC use enhanced performance of educational activities in the surgery clerkship. Effort toward developing educational software for surgical students is warranted because students are likely to use such programs.

The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

A systematic literature review of open source software quality assessment models.

PubMed

Adewumi, Adewole; Misra, Sanjay; Omoregbe, Nicholas; Crawford, Broderick; Soto, Ricardo

2016-01-01

Many open source software (OSS) quality assessment models are proposed and available in the literature. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their specific properties. Based on this, the aim of this study is to perform a systematic literature review to investigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formulation and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the first known OSS quality model emerged in 2003. A total of 19 OSS quality assessment model papers were selected. To select these models we have developed assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classified into five categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study reflects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47%) of the existing models do not specify any domain of application. In conclusion, our study will be a valuable contribution to the community and helps the quality assessment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives.

Data Publication and Interoperability for Long Tail Researchers via the Open Data Repository's (ODR) Data Publisher.

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R.; Downs, R. T.; Blake, D. F.; Fonda, M.; Pires, A.

2016-12-01

Working primarily with astrobiology researchers at NASA Ames, the Open Data Repository (ODR) has been conducting a software pilot to meet the varying needs of this multidisciplinary community. Astrobiology researchers often have small communities or operate individually with unique data sets that don't easily fit into existing database structures. The ODR constructed its Data Publisher software to allow researchers to create databases with common metadata structures and subsequently extend them to meet their individual needs and data requirements. The software accomplishes these tasks through a web-based interface that allows collaborative creation and revision of common metadata templates and individual extensions to these templates for custom data sets. This allows researchers to search disparate datasets based on common metadata established through the metadata tools, but still facilitates distinct analyses and data that may be stored alongside the required common metadata. The software produces web pages that can be made publicly available at the researcher's discretion so that users may search and browse the data in an effort to make interoperability and data discovery a human-friendly task while also providing semantic data for machine-based discovery. Once relevant data has been identified, researchers can utilize the built-in application programming interface (API) that exposes the data for machine-based consumption and integration with existing data analysis tools (e.g. R, MATLAB, Project Jupyter - http://jupyter.org). The current evolution of the project has created the Astrobiology Habitable Environments Database (AHED)[1] which provides an interface to databases connected through a common metadata core. In the next project phase, the goal is for small research teams and groups to be self-sufficient in publishing their research data to meet funding mandates and academic requirements as well as fostering increased data discovery and interoperability through human-readable and machine-readable interfaces. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, MSL. [1] B. Lafuente et al. (2016) AGU, submitted.

An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex

PubMed Central

Van Essen, David C.; Drury, Heather A.; Dickson, James; Harwell, John; Hanlon, Donna; Anderson, Charles H.

2001-01-01

The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database. PMID:11522765

Cloud parallel processing of tandem mass spectrometry based proteomics data.

PubMed

Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

2012-10-05

Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

PubMed

Peterson, Elena S; McCue, Lee Ann; Schrimpe-Rutledge, Alexandra C; Jensen, Jeffrey L; Walker, Hyunjoo; Kobold, Markus A; Webb, Samantha R; Payne, Samuel H; Ansong, Charles; Adkins, Joshua N; Cannon, William R; Webb-Robertson, Bobbie-Jo M

2012-04-05

The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

PubMed Central

2012-01-01

Background The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates. Results VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (Yersinia pestis Pestoides F and Synechococcus sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data. Conclusions VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at https://www.biopilot.org/docs/Software/Vespa.php. PMID:22480257

Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm.

PubMed

Oh, Cheolhwan; Huang, Xiaodong; Regnier, Fred E; Buck, Charles; Zhang, Xiang

2008-02-01

We report a novel peak sorting method for the two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/TOF-MS) system. The objective of peak sorting is to recognize peaks from the same metabolite occurring in different samples from thousands of peaks detected in the analytical procedure. The developed algorithm is based on the fact that the chromatographic peaks for a given analyte have similar retention times in all of the chromatograms. Raw instrument data are first processed by ChromaTOF (Leco) software to provide the peak tables. Our algorithm achieves peak sorting by utilizing the first- and second-dimension retention times in the peak tables and the mass spectra generated during the process of electron impact ionization. The algorithm searches the peak tables for the peaks generated by the same type of metabolite using several search criteria. Our software also includes options to eliminate non-target peaks from the sorting results, e.g., peaks of contaminants. The developed software package has been tested using a mixture of standard metabolites and another mixture of standard metabolites spiked into human serum. Manual validation demonstrates high accuracy of peak sorting with this algorithm.

Applying Hypertext Structures to Software Documentation.

ERIC Educational Resources Information Center

French, James C.; And Others

1997-01-01

Describes a prototype system for software documentation management called SLEUTH (Software Literacy Enhancing Usefulness to Humans) being developed at the University of Virginia. Highlights include information retrieval techniques, hypertext links that are installed automatically, a WAIS (Wide Area Information Server) search engine, user…

Mercury- Distributed Metadata Management, Data Discovery and Access System

NASA Astrophysics Data System (ADS)

Palanisamy, Giri; Wilson, Bruce E.; Devarakonda, Ranjeet; Green, James M.

2007-12-01

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source and ORNL- developed software. It was originally developed for NASA, and the Mercury development consortium now includes funding from NASA, USGS, and DOE. Mercury supports various metadata standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115 (under development). Mercury provides a single portal to information contained in disparate data management systems. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces then allow the users to perform simple, fielded, spatial and temporal searches across these metadata sources. This centralized repository of metadata with distributed data sources provides extremely fast search results to the user, while allowing data providers to advertise the availability of their data and maintain complete control and ownership of that data. Mercury supports various projects including: ORNL DAAC, NBII, DADDI, LBA, NARSTO, CDIAC, OCEAN, I3N, IAI, ESIP and ARM. The new Mercury system is based on a Service Oriented Architecture and supports various services such as Thesaurus Service, Gazetteer Web Service and UDDI Directory Services. This system also provides various search services including: RSS, Geo-RSS, OpenSearch, Web Services and Portlets. Other features include: Filtering and dynamic sorting of search results, book-markable search results, save, retrieve, and modify search criteria.

The environmental control and life support system advanced automation project. Phase 1: Application evaluation

NASA Technical Reports Server (NTRS)

Dewberry, Brandon S.

1990-01-01

The Environmental Control and Life Support System (ECLSS) is a Freedom Station distributed system with inherent applicability to advanced automation primarily due to the comparatively large reaction times of its subsystem processes. This allows longer contemplation times in which to form a more intelligent control strategy and to detect or prevent faults. The objective of the ECLSS Advanced Automation Project is to reduce the flight and ground manpower needed to support the initial and evolutionary ECLS system. The approach is to search out and make apparent those processes in the baseline system which are in need of more automatic control and fault detection strategies, to influence the ECLSS design by suggesting software hooks and hardware scars which will allow easy adaptation to advanced algorithms, and to develop complex software prototypes which fit into the ECLSS software architecture and will be shown in an ECLSS hardware testbed to increase the autonomy of the system. Covered here are the preliminary investigation and evaluation process, aimed at searching the ECLSS for candidate functions for automation and providing a software hooks and hardware scars analysis. This analysis shows changes needed in the baselined system for easy accommodation of knowledge-based or other complex implementations which, when integrated in flight or ground sustaining engineering architectures, will produce a more autonomous and fault tolerant Environmental Control and Life Support System.

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

Background High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/. PMID:23327565

Mining collections of compounds with Screening Assistant 2.

PubMed

Guilloux, Vincent Le; Arrault, Alban; Colliandre, Lionel; Bourg, Stéphane; Vayer, Philippe; Morin-Allory, Luc

2012-08-31

High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

Hybrid Differential Dynamic Programming with Stochastic Search

NASA Technical Reports Server (NTRS)

Aziz, Jonathan; Parker, Jeffrey; Englander, Jacob A.

2016-01-01

Differential dynamic programming (DDP) has been demonstrated as a viable approach to low-thrust trajectory optimization, namely with the recent success of NASA's Dawn mission. The Dawn trajectory was designed with the DDP-based Static/Dynamic Optimal Control algorithm used in the Mystic software.1 Another recently developed method, Hybrid Differential Dynamic Programming (HDDP),2, 3 is a variant of the standard DDP formulation that leverages both first-order and second-order state transition matrices in addition to nonlinear programming (NLP) techniques. Areas of improvement over standard DDP include constraint handling, convergence properties, continuous dynamics, and multi-phase capability. DDP is a gradient based method and will converge to a solution nearby an initial guess. In this study, monotonic basin hopping (MBH) is employed as a stochastic search method to overcome this limitation, by augmenting the HDDP algorithm for a wider search of the solution space.

From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library.

PubMed

Bietz, Stefan; Inhester, Therese; Lauck, Florian; Sommer, Kai; von Behren, Mathias M; Fährrolfes, Rainer; Flachsenberg, Florian; Meyder, Agnes; Nittinger, Eva; Otto, Thomas; Hilbig, Matthias; Schomburg, Karen T; Volkamer, Andrea; Rarey, Matthias

2017-11-10

Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformatics and cheminformatics, we provide software covering a wide range of research questions. Our all-in-one web service platform ProteinsPlus (http://proteins.plus) offers solutions for pocket and druggability prediction, hydrogen placement, structure quality assessment, ensemble generation, protein-protein interaction classification, and 2D-interaction visualization. Additionally, we provide a software package that contains tools targeting cheminformatics problems like file format conversion, molecule data set processing, SMARTS editing, fragment space enumeration, and ligand-based virtual screening. Furthermore, it also includes structural bioinformatics solutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries. The software package is available at http://software.zbh.uni-hamburg.de. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.

PubMed

Uszkoreit, Julian; Maerkens, Alexandra; Perez-Riverol, Yasset; Meyer, Helmut E; Marcus, Katrin; Stephan, Christian; Kohlbacher, Oliver; Eisenacher, Martin

2015-07-02

Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.

The Telecommunications and Data Acquisition Report

NASA Technical Reports Server (NTRS)

Posner, E. C. (Editor)

1986-01-01

This publication, one of a series formerly titled The Deep Space Network (DSN) Progress Report, documents DSN progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations. In addition, developments in Earth-based radio technology as applied to geodynamics, astrophysics, and the radio search for extraterrestrial intelligence are reported.

Analysing Culture and Interculture in Saudi EFL Textbooks: A Corpus Linguistic Approach

ERIC Educational Resources Information Center

Almujaiwel, Sultan

2018-01-01

This paper combines corpus processing tools to investigate the cultural elements of Saudi education of English as a foreign language (EFL). The latest Saudi EFL textbooks (2016 onwards) are available in researchable PDF formats. This helps process them through corpus search software tools. The method adopted is based on analysing 20 cultural…

The Telecommunications and Data Acquisition Report

NASA Technical Reports Server (NTRS)

Posner, E. C. (Editor)

1988-01-01

This publication, one of a series formerly titled The Deep Space Network Progress Report, documents DSN progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations. In addition, developments in earth-based radio technology as applied to geodynamics, astrophysics, and the radio search for extraterrestrial intelligence are reported.

Microsoft Licenses Berkeley Lab's Home Energy Saver Code for Its Energy

Science.gov Websites

-based tool for calculating energy use in residential buildings. About one million people visit the Home Management Software | Berkeley Lab Berkeley Lab A-Z Index Directory Submit Web People Navigation Berkeley Lab Search Submit Web People Close About the Lab Leadership/Organization Calendar News

The Telecommunications and Data Acquisition Report. [Deep Space Network

NASA Technical Reports Server (NTRS)

Posner, E. C. (Editor)

1986-01-01

This publication, one of a series formerly titled The Deep Space Network Progress Report, documents DSN progress in flight project support, tracking and data acquisition research and technology, network engineering, hardware and software implementation, and operations. In addition, developments in Earth-based radio technology as applied to geodynamics, astrophysics and the radio search for extraterrestrial intelligence are reported.

E-Learning Technologies: Employing Matlab Web Server to Facilitate the Education of Mathematical Programming

ERIC Educational Resources Information Center

Karagiannis, P.; Markelis, I.; Paparrizos, K.; Samaras, N.; Sifaleras, A.

2006-01-01

This paper presents new web-based educational software (webNetPro) for "Linear Network Programming." It includes many algorithms for "Network Optimization" problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such…

Mind Maps: Hot New Tools Proposed for Cyberspace Librarians.

ERIC Educational Resources Information Center

Humphreys, Nancy K.

1999-01-01

Describes how online searchers can use a software tool based on back-of-the-book indexes to assist in dealing with search engine databases compiled by spiders that crawl across the entire Internet or through large Web sites. Discusses human versus machine knowledge, conversion of indexes to mind maps or mini-thesauri, middleware, eXtensible Markup…

A search for Earth-crossing asteroids, supplement

NASA Technical Reports Server (NTRS)

Taff, L. G.; Sorvari, J. M.; Kostishack, D. F.

1984-01-01

The ground based electro-optical deep space surveillance program involves a network of computer controlled 40 inch 1m telescopes equipped with large format, low light level, television cameras of the intensified silicon diode array type which is to replace the Baker-Nunn photographic camera system for artificial satellite tracking. A prototype observatory was constructed where distant artificial satellites are discriminated from stars in real time on the basis of the satellites' proper motion. Hardware was modified and the technique was used to observe and search for minor planets. Asteroids are now routinely observed and searched. The complete observing cycle, including the 2"-3" measurement of position, requires about four minutes at present. The commonality of asteroids and artificial satellite observing, searching, data reduction, and orbital analysis is stressed. Improvements to the hardware and software as well as operational techniques are considered.

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.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

An Open Source Software and Web-GIS Based Platform for Airborne SAR Remote Sensing Data Management, Distribution and Sharing

NASA Astrophysics Data System (ADS)

Changyong, Dou; Huadong, Guo; Chunming, Han; Ming, Liu

2014-03-01

With more and more Earth observation data available to the community, how to manage and sharing these valuable remote sensing datasets is becoming an urgent issue to be solved. The web based Geographical Information Systems (GIS) technology provides a convenient way for the users in different locations to share and make use of the same dataset. In order to efficiently use the airborne Synthetic Aperture Radar (SAR) remote sensing data acquired in the Airborne Remote Sensing Center of the Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS), a Web-GIS based platform for airborne SAR data management, distribution and sharing was designed and developed. The major features of the system include map based navigation search interface, full resolution imagery shown overlaid the map, and all the software adopted in the platform are Open Source Software (OSS). The functions of the platform include browsing the imagery on the map navigation based interface, ordering and downloading data online, image dataset and user management, etc. At present, the system is under testing in RADI and will come to regular operation soon.

SAM: String-based sequence search algorithm for mitochondrial DNA database queries

PubMed Central

Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

2011-01-01

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

Updates to the Virtual Atomic and Molecular Data Centre

NASA Astrophysics Data System (ADS)

Hill, Christian; Tennyson, Jonathan; Gordon, Iouli E.; Rothman, Laurence S.; Dubernet, Marie-Lise

2014-06-01

The Virtual Atomic and Molecular Data Centre (VAMDC) has established a set of standards for the storage and transmission of atomic and molecular data and an SQL-based query language (VSS2) for searching online databases, known as nodes. The project has also created an online service, the VAMDC Portal, through which all of these databases may be searched and their results compared and aggregated. Since its inception four years ago, the VAMDC e-infrastructure has grown to encompass over 40 databases, including HITRAN, in more than 20 countries and engages actively with scientists in six continents. Associated with the portal are a growing suite of software tools for the transformation of data from its native, XML-based, XSAMS format, to a range of more convenient human-readable (such as HTML) and machinereadable (such as CSV) formats. The relational database for HITRAN1, created as part of the VAMDC project is a flexible and extensible data model which is able to represent a wider range of parameters than the current fixed-format text-based one. Over the next year, a new online interface to this database will be tested, released and fully documented - this web application, HITRANonline2, will fully replace the ageing and incomplete JavaHAWKS software suite.

An introduction to information retrieval: applications in genomics

PubMed Central

Nadkarni, P M

2011-01-01

Information retrieval (IR) is the field of computer science that deals with the processing of documents containing free text, so that they can be rapidly retrieved based on keywords specified in a user’s query. IR technology is the basis of Web-based search engines, and plays a vital role in biomedical research, because it is the foundation of software that supports literature search. Documents can be indexed by both the words they contain, as well as the concepts that can be matched to domain-specific thesauri; concept matching, however, poses several practical difficulties that make it unsuitable for use by itself. This article provides an introduction to IR and summarizes various applications of IR and related technologies to genomics. PMID:12049181

Computer Software for Intelligent Systems.

ERIC Educational Resources Information Center

Lenat, Douglas B.

1984-01-01

Discusses the development and nature of computer software for intelligent systems, indicating that the key to intelligent problem-solving lies in reducing the random search for solutions. Formal reasoning methods, expert systems, and sources of power in problem-solving are among the areas considered. Specific examples of such software are…

Where's My Data - WMD

NASA Technical Reports Server (NTRS)

Quach, William L.; Sesplaukis, Tadas; Owen-Mankovich, Kyran J.; Nakamura, Lori L.

2012-01-01

WMD provides a centralized interface to access data stored in the Mission Data Processing and Control System (MPCS) GDS (Ground Data Systems) databases during MSL (Mars Science Laboratory) Testbeds and ATLO (Assembly, Test, and Launch Operations) test sessions. The MSL project organizes its data based on venue (Testbed, ATLO, Ops), with each venue's data stored on a separate database, making it cumbersome for users to access data across the various venues. WMD allows sessions to be retrieved through a Web-based search using several criteria: host name, session start date, or session ID number. Sessions matching the search criteria will be displayed and users can then select a session to obtain and analyze the associated data. The uniqueness of this software comes from its collection of data retrieval and analysis features provided through a single interface. This allows users to obtain their data and perform the necessary analysis without having to worry about where and how to get the data, which may be stored in various locations. Additionally, this software is a Web application that only requires a standard browser without additional plug-ins, providing a cross-platform, lightweight solution for users to retrieve and analyze their data. This software solves the problem of efficiently and easily finding and retrieving data from thousands of MSL Testbed and ATLO sessions. WMD allows the user to retrieve their session in as little as one mouse click, and then to quickly retrieve additional data associated with the session.

Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing.

PubMed

Sorbello, Alfred; Ripple, Anna; Tonning, Joseph; Munoz, Monica; Hasan, Rashedul; Ly, Thomas; Francis, Henry; Bodenreider, Olivier

2017-03-22

We seek to develop a prototype software analytical tool to augment FDA regulatory reviewers' capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool. A prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use. All usability test participants cited the tool's ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool's automated literature search relative to a manual 'all fields' PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools. Usability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction.

The Perfectly Organized Search Service.

ERIC Educational Resources Information Center

Leach, Sandra Sinsel; Spencer, Mary Ellen

1993-01-01

Describes the evolution and operation of the successful Database Search Service (DSS) at the John C. Hodges Library, University of Tennessee, with detailed information about equipment, policies, software, training, and physical layout. Success is attributed to careful administration, standardization of search equipment and interfaces, staff…

Catalog Federation and Interoperability for Geoinformatics

NASA Astrophysics Data System (ADS)

Memon, A.; Lin, K.; Baru, C.

2008-12-01

With the increasing proliferation of online resources in the geosciences, including data, tools, and software services, there is also a proliferation of catalogs containing metadata that describe these resources. To realize the vision articulated in the NSF Workshop on Building a National Geoinformatics System, March 2007-where a user can sit at a terminal and easily search, discover, integrate and use distributed geoscience resources-it will be essential that a search request be able to traverse these multiple metadata catalogs. In this paper, we describe our effort at prototyping catalog interoperability across multiple metadata catalogs. An example of a metadata catalog is the one employed in the GEON Project (www.geongrid.org). The central GEON catalog can be searched using spatial, temporal, and other metadata-based search criteria. The search can be invoked as a Web service and, therefore, can be imbedded in any software application. There has been a requirement from some of the GEON collaborators (for example, at the University of Hyderabad, India and the Navajo Technical College, New Mexico) to deploy their own catalogs, to store information about their resources locally, while they publish some of this information for broader access and use. Thus, a search must now be able to span multiple, independent GEON catalogs. Next, some of our collaborators-e.g. GEO Grid (Global Earth Observations Grid) in Japan-are implementing the Catalog Services for the Web (CS-W) standard for their catalog, thereby requiring the search to span across catalogs implemented using the CS-W standard as well. Finally, we have recently deployed a search service to access all EarthScope data products, which are distributed across organizations in Seattle, WA (IRIS), Boulder, CO (UNAVCO), and Potsdam, Germany (ICDP/GFZ). This service essentially implements a virtual catalog (the actual catalogs and data are stored at the remote locations). So, there is the need to incorporate such 3rd party searches within a broader search function, such as GEONsearch in the GEON Portal. We will discuss technical issues involved in designing and deploying such a multi-catalog search service in GEON.

YBYRÁ facilitates comparison of large phylogenetic trees.

PubMed

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

The Widest Practicable Dissemination: The NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Binkley, Robert L.; Kellogg, Yvonne D.; Paulson, Sharon S.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael J.; Accomazzi, Alberto

1995-01-01

The National Aeronautics and Space Act of 1958 established NASA and charged it to "provide for the widest practicable and appropriate dissemination of information concerning [...] its activities and the results thereof." The search for innovative methods to distribute NASA s information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the services over the initial 6-month period. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained will allow NASA to ensure that its institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

The widest practicable dissemination: The NASA technical report server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Binkley, Robert L.; Kellogg, Yvonne D.; Paulson, Sharon S.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael J.; Accomazzi, Alberto

1995-01-01

The National Aeronautics and Space Act of 1958 established NASA and charged it to 'provide for the widest practicable and appropriate dissemination of information concerning...its activities and the results thereof.' The search for innovative methods to distribute NASA's information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the services over the initial six-month period. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained will allow NASA to ensure that its institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

Faceted Visualization of Three Dimensional Neuroanatomy By Combining Ontology with Faceted Search

PubMed Central

Veeraraghavan, Harini; Miller, James V.

2013-01-01

In this work, we present a faceted-search based approach for visualization of anatomy by combining a three dimensional digital atlas with an anatomy ontology. Specifically, our approach provides a drill-down search interface that exposes the relevant pieces of information (obtained by searching the ontology) for a user query. Hence, the user can produce visualizations starting with minimally specified queries. Furthermore, by automatically translating the user queries into the controlled terminology our approach eliminates the need for the user to use controlled terminology. We demonstrate the scalability of our approach using an abdominal atlas and the same ontology. We implemented our visualization tool on the opensource 3D Slicer software. We present results of our visualization approach by combining a modified Foundational Model of Anatomy (FMA) ontology with the Surgical Planning Laboratory (SPL) Brain 3D digital atlas, and geometric models specific to patients computed using the SPL brain tumor dataset. PMID:24006207

Faceted visualization of three dimensional neuroanatomy by combining ontology with faceted search.

PubMed

Veeraraghavan, Harini; Miller, James V

2014-04-01

In this work, we present a faceted-search based approach for visualization of anatomy by combining a three dimensional digital atlas with an anatomy ontology. Specifically, our approach provides a drill-down search interface that exposes the relevant pieces of information (obtained by searching the ontology) for a user query. Hence, the user can produce visualizations starting with minimally specified queries. Furthermore, by automatically translating the user queries into the controlled terminology our approach eliminates the need for the user to use controlled terminology. We demonstrate the scalability of our approach using an abdominal atlas and the same ontology. We implemented our visualization tool on the opensource 3D Slicer software. We present results of our visualization approach by combining a modified Foundational Model of Anatomy (FMA) ontology with the Surgical Planning Laboratory (SPL) Brain 3D digital atlas, and geometric models specific to patients computed using the SPL brain tumor dataset.

Software Repository

NASA Technical Reports Server (NTRS)

Merwarth, P., D.

1983-01-01

The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

31 CFR 560.538 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; and (ii) Exporting embedded software necessary... that the software is designated as “EAR99” under the Export Administration Regulations, 15 CFR parts...

31 CFR 538.529 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for... software is classified as “EAR 99” under the Export Administration Regulations, 15 CFR parts 730-774 (the...

31 CFR 560.538 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2013 CFR

2013-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; and (ii) Exporting embedded software necessary... that the software is designated as “EAR99” under the Export Administration Regulations, 15 CFR parts...

31 CFR 538.529 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2013 CFR

2013-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for... software is classified as “EAR 99” under the Export Administration Regulations, 15 CFR parts 730-774 (the...

31 CFR 538.529 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2011 CFR

2011-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for... software is classified as “EAR 99” under the Export Administration Regulations, 15 CFR parts 730-774 (the...

31 CFR 538.529 - Authorized transactions necessary and ordinarily incident to publishing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... written publication in electronic format, the addition of embedded software necessary for reading, browsing, navigating, or searching the written publication; (ii) Exporting embedded software necessary for... software is classified as “EAR 99” under the Export Administration Regulations, 15 CFR parts 730-774 (the...

Collaborative Software and Focused Distraction in the Classroom

ERIC Educational Resources Information Center

Rhine, Steve; Bailey, Mark

2011-01-01

In search of strategies for increasing their pre-service teachers' thoughtful engagement with content and in an effort to model connection between choice of technology and pedagogical goals, the authors utilized collaborative software during class time. Collaborative software allows all students to write simultaneously on a single collective…

Learn by Yourself: The Self-Learning Tools for Qualitative Analysis Software Packages

ERIC Educational Resources Information Center

Freitas, Fábio; Ribeiro, Jaime; Brandão, Catarina; Reis, Luís Paulo; de Souza, Francislê Neri; Costa, António Pedro

2017-01-01

Computer Assisted Qualitative Data Analysis Software (CAQDAS) are tools that help researchers to develop qualitative research projects. These software packages help the users with tasks such as transcription analysis, coding and text interpretation, writing and annotation, content search and analysis, recursive abstraction, grounded theory…

Reducing a Knowledge-Base Search Space When Data Are Missing

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

This software addresses the problem of how to efficiently execute a knowledge base in the presence of missing data. Computationally, this is an exponentially expensive operation that without heuristics generates a search space of 1 + 2n possible scenarios, where n is the number of rules in the knowledge base. Even for a knowledge base of the most modest size, say 16 rules, it would produce 65,537 possible scenarios. The purpose of this software is to reduce the complexity of this operation to a more manageable size. The problem that this system solves is to develop an automated approach that can reason in the presence of missing data. This is a meta-reasoning capability that repeatedly calls a diagnostic engine/model to provide prognoses and prognosis tracking. In the big picture, the scenario generator takes as its input the current state of a system, including probabilistic information from Data Forecasting. Using model-based reasoning techniques, it returns an ordered list of fault scenarios that could be generated from the current state, i.e., the plausible future failure modes of the system as it presently stands. The scenario generator models a Potential Fault Scenario (PFS) as a black box, the input of which is a set of states tagged with priorities and the output of which is one or more potential fault scenarios tagged by a confidence factor. The results from the system are used by a model-based diagnostician to predict the future health of the monitored system.

AstroCloud, a Cyber-Infrastructure for Astronomy Research: Data Access and Interoperability

NASA Astrophysics Data System (ADS)

Fan, D.; He, B.; Xiao, J.; Li, S.; Li, C.; Cui, C.; Yu, C.; Hong, Z.; Yin, S.; Wang, C.; Cao, Z.; Fan, Y.; Mi, L.; Wan, W.; Wang, J.

2015-09-01

Data access and interoperability module connects the observation proposals, data, virtual machines and software. According to the unique identifier of PI (principal investigator), an email address or an internal ID, data can be collected by PI's proposals, or by the search interfaces, e.g. conesearch. Files associated with the searched results could be easily transported to cloud storages, including the storage with virtual machines, or several commercial platforms like Dropbox. Benefitted from the standards of IVOA (International Observatories Alliance), VOTable formatted searching result could be sent to kinds of VO software. Latter endeavor will try to integrate more data and connect archives and some other astronomical resources.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

World Wide Web Metaphors for Search Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

PubMed Central

2012-01-01

Background For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. Results We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. Conclusion The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources. PMID:23216909

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.

PubMed

Lewis, Steven; Csordas, Attila; Killcoyne, Sarah; Hermjakob, Henning; Hoopmann, Michael R; Moritz, Robert L; Deutsch, Eric W; Boyle, John

2012-12-05

For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources.

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

Zhang, Guo-Qiang; Szymanski, Jacek; Wilson, David

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

The spectra program library: A PC based system for gamma-ray spectra analysis and INAA data reduction

USGS Publications Warehouse

Baedecker, P.A.; Grossman, J.N.

1995-01-01

A PC based system has been developed for the analysis of gamma-ray spectra and for the complete reduction of data from INAA experiments, including software to average the results from mulitple lines and multiple countings and to produce a final report of analysis. Graphics algorithms may be called for the analysis of complex spectral features, to compare the data from alternate photopeaks and to evaluate detector performance during a given counting cycle. A database of results for control samples can be used to prepare quality control charts to evaluate long term precision and to search for systemic variations in data on reference samples as a function of time. The entire software library can be accessed through a user-friendly menu interface with internal help.

A Practical Guide to Calibration of a GSSHA Hydrologic Model Using ERDC Automated Model Calibration Software - Efficient Local Search

DTIC Science & Technology

2012-02-01

use the ERDC software implementation of the secant LM method that accommodates the PEST model independent interface to calibrate a GSSHA...how the method works. We will also demonstrate how our LM/SLM implementation compares with its counterparts as implemented in the popular PEST ...function values and total model calls for local search to converge) associated with Examples 1 and 3 using the PEST LM/SLM implementations

Tautomerism in chemical information management systems

NASA Astrophysics Data System (ADS)

Warr, Wendy A.

2010-06-01

Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

Software Engineering Improvement Activities/Plan

NASA Technical Reports Server (NTRS)

2003-01-01

bd Systems personnel accomplished the technical responsibilities for this reporting period, as planned. A close working relationship was maintained with personnel of the MSFC Avionics Department Software Group (ED14). Work accomplishments included development, evaluation, and enhancement of a software cost model, performing literature search and evaluation of software tools available for code analysis and requirements analysis, and participating in other relevant software engineering activities. Monthly reports were submitted. This support was provided to the Flight Software Group/ED 1 4 in accomplishing the software engineering improvement engineering activities of the Marshall Space Flight Center (MSFC) Software Engineering Improvement Plan.

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

PubMed

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

2011-08-05

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

Tracking Positions and Attitudes of Mars Rovers

NASA Technical Reports Server (NTRS)

Ali, Khaled; vanelli, Charles; Biesiadecki, Jeffrey; Martin, Alejandro San; Maimone, Mark; Cheng, Yang; Alexander, James

2006-01-01

The Surface Attitude Position and Pointing (SAPP) software, which runs on computers aboard the Mars Exploration Rovers, tracks the positions and attitudes of the rovers on the surface of Mars. Each rover acquires data on attitude from a combination of accelerometer readings and images of the Sun acquired autonomously, using a pointable camera to search the sky for the Sun. Depending on the nature of movement commanded remotely by operators on Earth, the software propagates attitude and position by use of either (1) accelerometer and gyroscope readings or (2) gyroscope readings and wheel odometry. Where necessary, visual odometry is performed on images to fine-tune the position updates, particularly on high-wheel-slip terrain. The attitude data are used by other software and ground-based personnel for pointing a high-gain antenna, planning and execution of driving, and positioning and aiming scientific instruments.

ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.

PubMed

Lou, Shao-Ke; Ni, Bing; Lo, Leung-Yau; Tsui, Stephen Kwok-Wing; Chan, Ting-Fung; Leung, Kwong-Sak

2011-02-01

Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature. The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.

Searching Lexis and Westlaw: Part III.

ERIC Educational Resources Information Center

Franklin, Carl

1986-01-01

This last installment in a three-part series covers several important areas in the searching of legal information: online (group) training and customer service, documentation (search manuals and other aids), account representatives, microcomputer software, and pricing. Advantages and drawbacks of both the LEXIS and WESTLAW databases are noted.…

Scaffolding software: How does it influence student conceptual understanding and motivation?

NASA Astrophysics Data System (ADS)

Butler, Kyle A.

The purpose of this study was to determine the influence of scaffolding software on student conceptual understanding and motivation. This study also provides insight on how students use the scaffolding features found in Artemis and the extent to which features show a relationship to student conceptual understanding and motivation. A Randomized Solomon Four Group Design was used in this study. As students worked through a project based unit over photosynthesis, the students performed information seeking activities that were based on their own inquiry. For this purpose, the students in the experimental group used an example of scaffolding software called Artemis, while the students in the control group used a search engine of their choice. To measure conceptual understanding, the researcher analyzed student generated concept maps on photosynthesis using three different methods (quantitative, qualitative, hierarchical). To measure motivation, the researcher used a survey that measured motivation on five different indicators: intrinsic goal orientation, extrinsic goal orientation, task value, control of learning beliefs, self-efficacy for learning and performance. Finally, the researcher looked at the relationship and influence of the scaffolding features on two student performance scores at the end of the unit. This created a total of ten dependent variables in relationship to the treatment. Overall, the students used the collaborative features 25% of the time, the maintenance features 0.84% of the time, the organizational features 16% of the time, the saving/viewing features 7% of the time and the searching features 51% of the time. There were significant correlations between the saving/viewing features hits and the students' task value (r = .499, p < .05), the searching features hits and the students' self-efficacy for learning and performance (r = .553, p < .01), the collaborative features hits and the students' essay performance scores (r = .519, p < .05) and the maintenance features time and the qualitative analysis of the concept maps (r = .576, p < .01). Finally, the results indicated that the scaffolding features in Artemis did not influence student conceptual understanding and motivation.

Laptop Computer - Based Facial Recognition System Assessment

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

R. A. Cain; G. B. Singleton

2001-03-01

The objective of this project was to assess the performance of the leading commercial-off-the-shelf (COTS) facial recognition software package when used as a laptop application. We performed the assessment to determine the system's usefulness for enrolling facial images in a database from remote locations and conducting real-time searches against a database of previously enrolled images. The assessment involved creating a database of 40 images and conducting 2 series of tests to determine the product's ability to recognize and match subject faces under varying conditions. This report describes the test results and includes a description of the factors affecting the results.more » After an extensive market survey, we selected Visionics' FaceIt{reg_sign} software package for evaluation and a review of the Facial Recognition Vendor Test 2000 (FRVT 2000). This test was co-sponsored by the US Department of Defense (DOD) Counterdrug Technology Development Program Office, the National Institute of Justice, and the Defense Advanced Research Projects Agency (DARPA). Administered in May-June 2000, the FRVT 2000 assessed the capabilities of facial recognition systems that were currently available for purchase on the US market. Our selection of this Visionics product does not indicate that it is the ''best'' facial recognition software package for all uses. It was the most appropriate package based on the specific applications and requirements for this specific application. In this assessment, the system configuration was evaluated for effectiveness in identifying individuals by searching for facial images captured from video displays against those stored in a facial image database. An additional criterion was that the system be capable of operating discretely. For this application, an operational facial recognition system would consist of one central computer hosting the master image database with multiple standalone systems configured with duplicates of the master operating in remote locations. Remote users could perform real-time searches where network connectivity is not available. As images are enrolled at the remote locations, periodic database synchronization is necessary.« less

PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing.

PubMed

Rastogi, Achal; Murik, Omer; Bowler, Chris; Tirichine, Leila

2016-07-01

With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an efficient and accurate reverse genetic tool for genome editing. Several computational tools have been published allowing researchers to find candidate target sequences for the engineering of the CRISPR vectors, while searching possible off-targets for the predicted candidates. These tools provide built-in genome databases of common model organisms that are used for CRISPR target prediction. Although their predictions are highly sensitive, the applicability to non-model genomes, most notably protists, makes their design inadequate. This motivated us to design a new CRISPR target finding tool, PhytoCRISP-Ex. Our software offers CRIPSR target predictions using an extended list of phytoplankton genomes and also delivers a user-friendly standalone application that can be used for any genome. The software attempts to integrate, for the first time, most available phytoplankton genomes information and provide a web-based platform for Cas9 target prediction within them with high sensitivity. By offering a standalone version, PhytoCRISP-Ex maintains an independence to be used with any organism and widens its applicability in high throughput pipelines. PhytoCRISP-Ex out pars all the existing tools by computing the availability of restriction sites over the most probable Cas9 cleavage sites, which can be ideal for mutant screens. PhytoCRISP-Ex is a simple, fast and accurate web interface with 13 pre-indexed and presently updating phytoplankton genomes. The software was also designed as a UNIX-based standalone application that allows the user to search for target sequences in the genomes of a variety of other species.

From Print to Pixels: Practitioners' Reflections on the Use of Qualitative Data Analysis Software.

ERIC Educational Resources Information Center

Gilbert, Linda S.

This paper studied how individual qualitative researchers perceive that their research procedures and perspectives have been influenced by the adoption of computer assisted qualitative data software. The study focused on Nud*Ist software (non-numerical Unstructured Data; Indexing, Searching, and Theorizing). The seven participants ranged from new…

Is Software Available for Early Childhood Spanish Speaking Children?

ERIC Educational Resources Information Center

Cardona de Divale, Maria Victoria

A search was conducted on the Internet for software available for bilingual Spanish-speaking children. The only programs found under this heading were 18 programs for learning Spanish. Five of the least expensive were selected for review using a standardized scale for evaluating children's software. Four of the programs were found to be…

Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT.

PubMed

Lessel, Uta; Wellenzohn, Bernd; Fischer, J Robert; Rarey, Matthias

2012-02-27

A case study is presented illustrating the design of a focused CDK2 library. The scaffold of the library was detected by a feature trees search in a fragment space based on reactions from combinatorial chemistry. For the design the software LoFT (Library optimizer using Feature Trees) was used. The special feature called FTMatch was applied to restrict the parts of the queries where the reagents are permitted to match. This way a 3D scoring function could be simulated. Results were compared with alternative designs by GOLD docking and ROCS 3D alignments.

Application of ChemDraw NMR Tool: Correlation of Program-Generated 13C Chemical Shifts and pKa Values of para-Substituted Benzoic Acids

NASA Astrophysics Data System (ADS)

Wang, Hongyi

2005-09-01

An application of ChemDraw NMR Tool was demonstrated by correlation of program-generated 13 C NMR chemical shifts and p K a values of para-substituted benzoic acids. Experimental 13 C NMR chemical shifts were analyzed in the same way for comparison. The project can be used as an assignment at the end of the first-year organic chemistry course to review topics or explore new techniques: Hammett equation, acid base equilibrium theory, electronic nature of functional groups, inductive and resonance effects, structure reactivity relationship, NMR spectroscopy, literature search, database search, and ChemDraw software.

Computer-aided diagnosis software for vulvovaginal candidiasis detection from Pap smear images.

PubMed

Momenzadeh, Mohammadreza; Vard, Alireza; Talebi, Ardeshir; Mehri Dehnavi, Alireza; Rabbani, Hossein

2018-01-01

Vulvovaginal candidiasis (VVC) is a common gynecologic infection and it occurs when there is overgrowth of the yeast called Candida. VVC diagnosis is usually done by observing a Pap smear sample under a microscope and searching for the conidium and mycelium components of Candida. This manual method is time consuming, subjective and tedious. Any diagnosis tools that detect VVC, semi- or full-automatically, can be very helpful to pathologists. This article presents a computer aided diagnosis (CAD) software to improve human diagnosis of VVC from Pap smear samples. The proposed software is designed based on phenotypic and morphology features of the Candida in Pap smear sample images. This software provide a user-friendly interface which consists of a set of image processing tools and analytical results that helps to detect Candida and determine severity of illness. The software was evaluated on 200 Pap smear sample images and obtained specificity of 91.04% and sensitivity of 92.48% to detect VVC. As a result, the use of the proposed software reduces diagnostic time and can be employed as a second objective opinion for pathologists. © 2017 Wiley Periodicals, Inc.

XML Flight/Ground Data Dictionary Management

NASA Technical Reports Server (NTRS)

Wright, Jesse; Wiklow, Colette

2007-01-01

A computer program generates Extensible Markup Language (XML) files that effect coupling between the command- and telemetry-handling software running aboard a spacecraft and the corresponding software running in ground support systems. The XML files are produced by use of information from the flight software and from flight-system engineering. The XML files are converted to legacy ground-system data formats for command and telemetry, transformed into Web-based and printed documentation, and used in developing new ground-system data-handling software. Previously, the information about telemetry and command was scattered in various paper documents that were not synchronized. The process of searching and reading the documents was time-consuming and introduced errors. In contrast, the XML files contain all of the information in one place. XML structures can evolve in such a manner as to enable the addition, to the XML files, of the metadata necessary to track the changes and the associated documentation. The use of this software has reduced the extent of manual operations in developing a ground data system, thereby saving considerable time and removing errors that previously arose in the translation and transcription of software information from the flight to the ground system.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

Mobile medical visual information retrieval.

PubMed

Depeursinge, Adrien; Duc, Samuel; Eggel, Ivan; Müller, Henning

2012-01-01

In this paper, we propose mobile access to peer-reviewed medical information based on textual search and content-based visual image retrieval. Web-based interfaces designed for limited screen space were developed to query via web services a medical information retrieval engine optimizing the amount of data to be transferred in wireless form. Visual and textual retrieval engines with state-of-the-art performance were integrated. Results obtained show a good usability of the software. Future use in clinical environments has the potential of increasing quality of patient care through bedside access to the medical literature in context.

Contract-Based Integration of Cyber-Physical Analyses

DTIC Science & Technology

2014-10-14

Conference on Embedded Software Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is...estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the ...data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this

Searching for Information Online: Using Big Data to Identify the Concerns of Potential Army Recruits

DTIC Science & Technology

2016-01-01

software. For instance, such Internet search engines as Google or Yahoo! often gather anonymized data regarding the topics that people search for, as...suggesting that these and other information needs may be fur- ther reflected in usage of online search engines . Google makes aggregated and anonymized...Internet search engines such as Google or Yahoo! often gather anonymized data regarding the topics that people search for, as well as the date and

Online Patent Searching: Guided by an Expert System.

ERIC Educational Resources Information Center

Ardis, Susan B.

1990-01-01

Describes the development of an expert system for online patent searching that uses menu driven software to interpret the user's knowledge level and the general nature of the search problem. The discussion covers the rationale for developing such a system, current system functions, cost effectiveness, user reactions, and plans for future…

Online Searching at 9600 Baud.

ERIC Educational Resources Information Center

Scott, Ralph Lee; Scott, Nancy Sue Schell

1991-01-01

Discusses online searching with the new 9600 baud rate and describes test searches on the BRS, Data-Star, LEXIS, and Dow Jones databases through three packet-switching networks: US Sprint, MEADNET, and TYMNET. Hardware and software are described, data communications equipment standards are discussed, and the impact of higher baud rates on pricing…

Speeding up the screening of steroids in urine: development of a user-friendly library.

PubMed

Galesio, M; López-Fdez, H; Reboiro-Jato, M; Gómez-Meire, Silvana; Glez-Peña, D; Fdez-Riverola, F; Lodeiro, Carlos; Diniz, M E; Capelo, J L

2013-12-11

This work presents a novel database search engine - MLibrary - designed to assist the user in the detection and identification of androgenic anabolic steroids (AAS) and its metabolites by matrix assisted laser desorption/ionization (MALDI) and mass spectrometry-based strategies. The detection of the AAS in the samples was accomplished by searching (i) the mass spectrometric (MS) spectra against the library developed to identify possible positives and (ii) by comparison of the tandem mass spectrometric (MS/MS) spectra produced after fragmentation of the possible positives with a complete set of spectra that have previously been assigned to the software. The urinary screening for anabolic agents plays a major role in anti-doping laboratories as they represent the most abused drug class in sports. With the help of the MLibrary software application, the use of MALDI techniques for doping control is simplified and the time for evaluation and interpretation of the results is reduced. To do so, the search engine takes as input several MALDI-TOF-MS and MALDI-TOF-MS/MS spectra. It aids the researcher in an automatic mode by identifying possible positives in a single MS analysis and then confirming their presence in tandem MS analysis by comparing the experimental tandem mass spectrometric data with the database. Furthermore, the search engine can, potentially, be further expanded to other compounds in addition to AASs. The applicability of the MLibrary tool is shown through the analysis of spiked urine samples. Copyright © 2013 Elsevier Inc. All rights reserved.

A design for a reusable Ada library

NASA Technical Reports Server (NTRS)

Litke, John D.

1986-01-01

A goal of the Ada language standardization effort is to promote reuse of software, implying the existence of substantial software libraries and the storage/retrieval mechanisms to support them. A searching/cataloging mechanism is proposed that permits full or partial distribution of the database, adapts to a variety of searching mechanisms, permits a changine taxonomy with minimal disruption, and minimizes the requirement of specialized cataloger/indexer skills. The important observation is that key words serve not only as indexing mechanism, but also as an identification mechanism, especially via concatenation and as support for a searching mechanism. By deliberately separating these multiple uses, the modifiability and ease of growth that current libraries require, is achieved.

A systematic review of healthcare applications for smartphones.

PubMed

Mosa, Abu Saleh Mohammad; Yoo, Illhoi; Sheets, Lincoln

2012-07-10

Advanced mobile communications and portable computation are now combined in handheld devices called "smartphones", which are also capable of running third-party software. The number of smartphone users is growing rapidly, including among healthcare professionals. The purpose of this study was to classify smartphone-based healthcare technologies as discussed in academic literature according to their functionalities, and summarize articles in each category. In April 2011, MEDLINE was searched to identify articles that discussed the design, development, evaluation, or use of smartphone-based software for healthcare professionals, medical or nursing students, or patients. A total of 55 articles discussing 83 applications were selected for this study from 2,894 articles initially obtained from the MEDLINE searches. A total of 83 applications were documented: 57 applications for healthcare professionals focusing on disease diagnosis (21), drug reference (6), medical calculators (8), literature search (6), clinical communication (3), Hospital Information System (HIS) client applications (4), medical training (2) and general healthcare applications (7); 11 applications for medical or nursing students focusing on medical education; and 15 applications for patients focusing on disease management with chronic illness (6), ENT-related (4), fall-related (3), and two other conditions (2). The disease diagnosis, drug reference, and medical calculator applications were reported as most useful by healthcare professionals and medical or nursing students. Many medical applications for smartphones have been developed and widely used by health professionals and patients. The use of smartphones is getting more attention in healthcare day by day. Medical applications make smartphones useful tools in the practice of evidence-based medicine at the point of care, in addition to their use in mobile clinical communication. Also, smartphones can play a very important role in patient education, disease self-management, and remote monitoring of patients.

A Systematic Review of Healthcare Applications for Smartphones

PubMed Central

2012-01-01

Background Advanced mobile communications and portable computation are now combined in handheld devices called “smartphones”, which are also capable of running third-party software. The number of smartphone users is growing rapidly, including among healthcare professionals. The purpose of this study was to classify smartphone-based healthcare technologies as discussed in academic literature according to their functionalities, and summarize articles in each category. Methods In April 2011, MEDLINE was searched to identify articles that discussed the design, development, evaluation, or use of smartphone-based software for healthcare professionals, medical or nursing students, or patients. A total of 55 articles discussing 83 applications were selected for this study from 2,894 articles initially obtained from the MEDLINE searches. Results A total of 83 applications were documented: 57 applications for healthcare professionals focusing on disease diagnosis (21), drug reference (6), medical calculators (8), literature search (6), clinical communication (3), Hospital Information System (HIS) client applications (4), medical training (2) and general healthcare applications (7); 11 applications for medical or nursing students focusing on medical education; and 15 applications for patients focusing on disease management with chronic illness (6), ENT-related (4), fall-related (3), and two other conditions (2). The disease diagnosis, drug reference, and medical calculator applications were reported as most useful by healthcare professionals and medical or nursing students. Conclusions Many medical applications for smartphones have been developed and widely used by health professionals and patients. The use of smartphones is getting more attention in healthcare day by day. Medical applications make smartphones useful tools in the practice of evidence-based medicine at the point of care, in addition to their use in mobile clinical communication. Also, smartphones can play a very important role in patient education, disease self-management, and remote monitoring of patients. PMID:22781312

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

PubMed

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

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

Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

2007-01-01

The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

The Preliminary Results of GMSTech: A Software Development for Microseismic Characterization

NASA Astrophysics Data System (ADS)

Rohaman, Maman; Suhendi, Cahli; Verdhora Ry, Rexha; Sugiartono Prabowo, Billy; Widiyantoro, Sri; Nugraha, Andri Dian; Yudistira, Tedi; Mujihardi, Bambang

2017-04-01

The processing of microseismic data requires reliable software for imaging the condition of subsurface related to occurring microseismicity. In general, the currently available software is only specific for certain processing module and developed by the different developer. However, the software with integrated processing modules will give a better value because the users can use it easier and faster. We developed GMSTech (Ganesha Microseismic Technology), a C# language-based standing-alone software consisting several modules for processing of microseismic data. Its function is to solve a non-linear inverse problem and imaging the subsurface. C# library is supported by ILNumerics to reduce time consumption and give good visualization. In this preliminary result, we will present four developed modules: (1) hypocenter determination, (2) moment magnitude calculation, and (3) 3D seismic tomography. In the first module, we provide four methods for locating the microseismic events that can be chosen by a user independently: simulated annealing method, guided grid-search method, Geiger’s method, and joint hypocenter determination (JHD). The second module can be used for calculating moment magnitude using Brune method and to estimate the released energy of the event. At last, we also provided the module of 3-D seismic tomography for imaging the velocity structures based on delay time tomography. We demonstrated the software using both a synthetic data and a real data from a certain geothermal field in Indonesia. The results for all modules are reliable and remarkable, reviewed statistically by RMS error. We will keep examining the software using another set of data and developing further modules of processing.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Liebetreu, John; Moore, Michael S.; Price, Jeremy C.; Abbott, Ben

2005-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Moore, Michael S.; Price, Jeremy C.; Abbott, Ben; Liebetreu, John; Reinhart, Richard C.; Kacpura, Thomas J.

2007-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

78 FR 76121 - Applications for New Awards; National Institute on Disability and Rehabilitation Research-Small...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-16

... information technology including cloud computing, software, systems, and devices that promote access to... using the article search feature at: www.federalregister.gov . Specifically, through the advanced search...

Books for the Job Hunt.

ERIC Educational Resources Information Center

Saltzman, Amy

1992-01-01

Reviews new and classic titles on career choice, job search methods, executive/professional job search, resume writing, and interviewing. Advises avoiding books with simplistic formulas and exercises or overt sales pitches for software, videos, and other products. (SK)

Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening

PubMed Central

Wang, Zhao; Lu, Yan; Seibel, William; Miller, Duane D.; Li, Wei

2009-01-01

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: 1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and 2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma. PMID:19445498

A Search Engine That's Aware of Your Needs

NASA Technical Reports Server (NTRS)

2005-01-01

Internet research can be compared to trying to drink from a firehose. Such a wealth of information is available that even the simplest inquiry can sometimes generate tens of thousands of leads, more information than most people can handle, and more burdensome than most can endure. Like everyone else, NASA scientists rely on the Internet as a primary search tool. Unlike the average user, though, NASA scientists perform some pretty sophisticated, involved research. To help manage the Internet and to allow researchers at NASA to gain better, more efficient access to the wealth of information, the Agency needed a search tool that was more refined and intelligent than the typical search engine. Partnership NASA funded Stottler Henke, Inc., of San Mateo, California, a cutting-edge software company, with a Small Business Innovation Research (SBIR) contract to develop the Aware software for searching through the vast stores of knowledge quickly and efficiently. The partnership was through NASA s Ames Research Center.

Communication Webagogy 2.0: More Click, Less Drag.

ERIC Educational Resources Information Center

Radford, Marie L.; Wagner, Kurt W.

2000-01-01

Argues that, because of the chaotic nature of the Web and the competing searching software, no single search tool will suffice. Lists and discusses meta search engines; communication meta-sites and subject directories, all indexed by humans; teaching resources for communication courses that utilize the unique features of the Web; and web sites…

Co Modeling and Co Synthesis of Safety Critical Multi threaded Embedded Software for Multi Core Embedded Platforms

DTIC Science & Technology

2017-03-20

computation, Prime Implicates, Boolean Abstraction, real- time embedded software, software synthesis, correct by construction software design , model...types for time -dependent data-flow networks". J.-P. Talpin, P. Jouvelot, S. Shukla. ACM-IEEE Conference on Methods and Models for System Design ...information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing   data sources, gathering and

Exhaustive search system and method using space-filling curves

DOEpatents

Spires, Shannon V.

2003-10-21

A search system and method for one agent or for multiple agents using a space-filling curve provides a way to control one or more agents to cover an area of any space of any dimensionality using an exhaustive search pattern. An example of the space-filling curve is a Hilbert curve. The search area can be a physical geography, a cyberspace search area, or an area searchable by computing resources. The search agent can be one or more physical agents, such as a robot, and can be software agents for searching cyberspace.

HTAPP: High-Throughput Autonomous Proteomic Pipeline

PubMed Central

Yu, Kebing; Salomon, Arthur R.

2011-01-01

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

The Chandra X-ray Center data system: supporting the mission of the Chandra X-ray Observatory

NASA Astrophysics Data System (ADS)

Evans, Janet D.; Cresitello-Dittmar, Mark; Doe, Stephen; Evans, Ian; Fabbiano, Giuseppina; Germain, Gregg; Glotfelty, Kenny; Hall, Diane; Plummer, David; Zografou, Panagoula

2006-06-01

The Chandra X-ray Center Data System provides end-to-end scientific software support for Chandra X-ray Observatory mission operations. The data system includes the following components: (1) observers' science proposal planning tools; (2) science mission planning tools; (3) science data processing, monitoring, and trending pipelines and tools; and (4) data archive and database management. A subset of the science data processing component is ported to multiple platforms and distributed to end-users as a portable data analysis package. Web-based user tools are also available for data archive search and retrieval. We describe the overall architecture of the data system and its component pieces, and consider the design choices and their impacts on maintainability. We discuss the many challenges involved in maintaining a large, mission-critical software system with limited resources. These challenges include managing continually changing software requirements and ensuring the integrity of the data system and resulting data products while being highly responsive to the needs of the project. We describe our use of COTS and OTS software at the subsystem and component levels, our methods for managing multiple release builds, and adapting a large code base to new hardware and software platforms. We review our experiences during the life of the mission so-far, and our approaches for keeping a small, but highly talented, development team engaged during the maintenance phase of a mission.

Software Tools Streamline Project Management

NASA Technical Reports Server (NTRS)

2009-01-01

Three innovative software inventions from Ames Research Center (NETMARK, Program Management Tool, and Query-Based Document Management) are finding their way into NASA missions as well as industry applications. The first, NETMARK, is a program that enables integrated searching of data stored in a variety of databases and documents, meaning that users no longer have to look in several places for related information. NETMARK allows users to search and query information across all of these sources in one step. This cross-cutting capability in information analysis has exponentially reduced the amount of time needed to mine data from days or weeks to mere seconds. NETMARK has been used widely throughout NASA, enabling this automatic integration of information across many documents and databases. NASA projects that use NETMARK include the internal reporting system and project performance dashboard, Erasmus, NASA s enterprise management tool, which enhances organizational collaboration and information sharing through document routing and review; the Integrated Financial Management Program; International Space Station Knowledge Management; Mishap and Anomaly Information Reporting System; and management of the Mars Exploration Rovers. Approximately $1 billion worth of NASA s projects are currently managed using Program Management Tool (PMT), which is based on NETMARK. PMT is a comprehensive, Web-enabled application tool used to assist program and project managers within NASA enterprises in monitoring, disseminating, and tracking the progress of program and project milestones and other relevant resources. The PMT consists of an integrated knowledge repository built upon advanced enterprise-wide database integration techniques and the latest Web-enabled technologies. The current system is in a pilot operational mode allowing users to automatically manage, track, define, update, and view customizable milestone objectives and goals. The third software invention, Query-Based Document Management (QBDM) is a tool that enables content or context searches, either simple or hierarchical, across a variety of databases. The system enables users to specify notification subscriptions where they associate "contexts of interest" and "events of interest" to one or more documents or collection(s) of documents. Based on these subscriptions, users receive notification when the events of interest occur within the contexts of interest for associated document or collection(s) of documents. Users can also associate at least one notification time as part of the notification subscription, with at least one option for the time period of notifications.

Evaluating and Mitigating the Impact of Complexity in Software Models

DTIC Science & Technology

2015-12-01

Internal use:* Permission to reproduce this material and to prepare derivative works from this material for internal use is granted, provided the...introduction) provides our motivation to study complexity and the essential re- search questions that we address in this effort. Some background information... provides the reader with a basis for the work and related areas explored. Section 2 (The Impact of Complexity) discusses the impact of model-based

The Joint Effects-Based Contracting Execution System: A Proposed Enabling Concept for Future Joint Expeditionary Contracting Execution

DTIC Science & Technology

2008-12-01

average 1 hour per response, including the time for reviewing instruction, searching existing data sources , gathering and maintaining the data needed...Representative for the Contracting Officer on five contracts whose value xii exceeded $200 million and participated on four source selection committees...roles on source selection boards; Consolidated Husbanding Services for all Pacific Ports, Consolidated MWR services for the Pacific, Software

A strategy for electronic dissemination of NASA Langley technical publications

NASA Technical Reports Server (NTRS)

Roper, Donna G.; Mccaskill, Mary K.; Holland, Scott D.; Walsh, Joanne L.; Nelson, Michael L.; Adkins, Susan L.; Ambur, Manjula Y.; Campbell, Bryan A.

1994-01-01

To demonstrate NASA Langley Research Center's relevance and to transfer technology to external customers in a timely and efficient manner, Langley has formed a working group to study and recommend a course of action for the electronic dissemination of technical reports (EDTR). The working group identified electronic report requirements (e.g., accessibility, file format, search requirements) of customers in U.S. industry through numerous site visits and personal contacts. Internal surveys were also used to determine commonalities in document preparation methods. From these surveys, a set of requirements for an electronic dissemination system was developed. Two candidate systems were identified and evaluated against the set of requirements: the Full-Text Electronic Documents System (FEDS), which is a full-text retrieval system based on the commercial document management package Interleaf, and the Langley Technical Report Server (LTRS), which is a Langley-developed system based on the publicly available World Wide Web (WWW) software system. Factors that led to the selection of LTRS as the vehicle for electronic dissemination included searching and viewing capability, current system operability, and client software availability for multiple platforms at no cost to industry. This report includes the survey results, evaluations, a description of the LTRS architecture, recommended policy statement, and suggestions for future implementations.

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.

PubMed

Mader, Malte; Simon, Ronald; Steinbiss, Sascha; Kurtz, Stefan

2011-07-28

The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle.

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

PubMed Central

2011-01-01

Background The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. Results We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. Conclusions FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle. PMID:21884636

Surveying the Numeric Databanks.

ERIC Educational Resources Information Center

O'Leary, Mick

1987-01-01

Describes six leading numeric databank services and compares them with bibliographic databases in terms of customers' needs, search software, pricing arrangements, and the role of the search specialist. A listing of the locations of the numeric databanks discussed is provided. (CLB)

GeneXplorer: an interactive web application for microarray data visualization and analysis.

PubMed

Rees, Christian A; Demeter, Janos; Matese, John C; Botstein, David; Sherlock, Gavin

2004-10-01

When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

Integrating query of relational and textual data in clinical databases: a case study.

PubMed

Fisk, John M; Mutalik, Pradeep; Levin, Forrest W; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Results are relevance-ranked using either "total documents per patient" or "report type weighting." Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers.

GlobiPack v. 1.0

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

Bartlett, Roscoe

2010-03-31

GlobiPack contains a small collection of optimization globalization algorithms. These algorithms are used by optimization and various nonlinear equation solver algorithms.Used as the line-search procedure with Newton and Quasi-Newton optimization and nonlinear equation solver methods. These are standard published 1-D line search algorithms such as are described in the book Nocedal and Wright Numerical Optimization: 2nd edition, 2006. One set of algorithms were copied and refactored from the existing open-source Trilinos package MOOCHO where the linear search code is used to globalize SQP methods. This software is generic to any mathematical optimization problem where smooth derivatives exist. There is nomore » specific connection or mention whatsoever to any specific application, period. You cannot find more general mathematical software.« less

Software Patents.

ERIC Educational Resources Information Center

Burke, Edmund B.

1994-01-01

Outlines basic patent law information that pertains to computer software programs. Topics addressed include protection in other countries; how to obtain patents; kinds of patents; duration; classes of patentable subject matter, including machines and processes; patentability searches; experimental use prior to obtaining a patent; and patent…

Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces.

PubMed

Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian

2008-04-24

Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.

A new nonlinear conjugate gradient coefficient under strong Wolfe-Powell line search

NASA Astrophysics Data System (ADS)

Mohamed, Nur Syarafina; Mamat, Mustafa; Rivaie, Mohd

2017-08-01

A nonlinear conjugate gradient method (CG) plays an important role in solving a large-scale unconstrained optimization problem. This method is widely used due to its simplicity. The method is known to possess sufficient descend condition and global convergence properties. In this paper, a new nonlinear of CG coefficient βk is presented by employing the Strong Wolfe-Powell inexact line search. The new βk performance is tested based on number of iterations and central processing unit (CPU) time by using MATLAB software with Intel Core i7-3470 CPU processor. Numerical experimental results show that the new βk converge rapidly compared to other classical CG method.

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

PubMed Central

Dowd, Scot E; Zaragoza, Joaquin; Rodriguez, Javier R; Oliver, Melvin J; Payton, Paxton R

2005-01-01

Background BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum. PMID:15819992

Pattern search in multi-structure data: a framework for the next-generation evidence-based medicine

NASA Astrophysics Data System (ADS)

Sukumar, Sreenivas R.; Ainsworth, Keela C.

2014-03-01

With the impetus towards personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledgebase, etc.) to predict diagnostic risks is fast emerging. Addressing this need, we pose and answer the following questions: (i) How can we jointly analyze and explore measurement data in context with qualitative domain knowledge? (ii) How can we search and hypothesize patterns (not known apriori) from such multi-structure data? (iii) How can we build predictive models by integrating weakly-associated multi-relational multi-structure data? We propose a framework towards answering these questions. We describe a software solution that leverages hardware for scalable in-memory analytics and applies next-generation semantic query tools on medical data.

Lessons in modern digital field geology: Open source software, 3D techniques, and the new world of digital mapping

NASA Astrophysics Data System (ADS)

Pavlis, Terry; Hurtado, Jose; Langford, Richard; Serpa, Laura

2014-05-01

Although many geologists refuse to admit it, it is time to put paper-based geologic mapping into the historical archives and move to the full potential of digital mapping techniques. For our group, flat map digital geologic mapping is now a routine operation in both research and instruction. Several software options are available, and basic proficiency with the software can be learned in a few hours of instruction and practice. The first practical field GIS software, ArcPad, remains a viable, stable option on Windows-based systems. However, the vendor seems to be moving away from ArcPad in favor of mobile software solutions that are difficult to implement without GIS specialists. Thus, we have pursued a second software option based on the open source program QGIS. Our QGIS system uses the same shapefile-centric data structure as our ArcPad system, including similar pop-up data entry forms and generic graphics for easy data management in the field. The advantage of QGIS is that the same software runs on virtually all common platforms except iOS, although the Android version remains unstable as of this writing. A third software option we are experimenting with for flat map-based field work is Fieldmove, a derivative of the 3D-capable program Move developed by Midland Valley. Our initial experiments with Fieldmove are positive, particularly with the new, inexpensive (<300Euros) Windows tablets. However, the lack of flexibility in data structure makes for cumbersome workflows when trying to interface our existing shapefile-centric data structures to Move. Nonetheless, in spring 2014 we will experiment with full-3D immersion in the field using the full Move software package in combination with ground based LiDAR and photogrammetry. One new workflow suggested by our initial experiments is that field geologists should consider using photogrammetry software to capture 3D visualizations of key outcrops. This process is now straightforward in several software packages, and it affords a previously unheard of potential for communicating the complexity of key exposures. For example, in studies of metamorphic structures we often search for days to find "Rosetta Stone" outcrops that display key geometric relationships. While conventional photographs rarely can capture the essence of the field exposure, capturing a true 3D representation of the exposure with multiple photos from many orientations can solve this communication problem. As spatial databases evolve these 3D models should be readily importable into the database.

Bill Calculator V1.0

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

2002-08-19

Utitlity tariffs vary significantly from utility to utility. Each utility has its own rates and sets of rules by which bills are calculated. The Bill Calculator reconstructs the tariff based on these rules, stored in data tables, and access the appropriate charges for a given energy consumption and demand. The software reconstructs the tariff logic from the rules stored in data tables. Changes are tallied as the logic is reconstructed. This is essentially an accounting program. The main limitation is on the time to search for each tariff element. It is currently on O(N) search. Also, since the Bill calculatormore » first stores all tariffs in an array and then reads the array to reconstruct a specific tariff, the memory limitatins of a particular system would limit the number of tariffs that could be handled. This tool allows a user to calculate a bill from any sampled utility without prior knowledge of the tariff logic or structure. The peculiarities of the tariff logic are stored in data tables and manged by the Bill Calculator software. This version of the software is implemented as a VB module that operates within Microsoft Excel. Input data tables are stored in Excel worksheets. In this version the Bill Calculator functions can be assessed through Excel as user defined worksheet functions. Bill Calculator can calculate approximately 50,000 bills in less than 30 minutes.« less

A PC-based software test for measuring alcohol and drug effects in human subjects.

PubMed

Mills, K C; Parkman, K M; Spruill, S E

1996-12-01

A new software-based visual search and divided-attention test of cognitive performance was developed and evaluated in an alcohol dose-response study with 24 human subjects aged 21-62 years. The test used language-free, color, graphic displays to represent the visuospatial demands of driving. Cognitive demands were increased over previous hardware-based tests, and the motor skills required for the test involved minimal eye movements and eye-hand coordination. Repeated performance on the test was evaluated with a latin-square design by using a placebo and two alcohol doses, low (0.48 g/kg/LBM) and moderate (0.72 g/kg/LBM). The data on 7 females and 17 males yielded significant falling and rising impairment effects coincident with moderate rising and falling breath alcohol levels (mean peak BrALs = 0.045 g/dl and 0.079 g/dl). None of the subjects reported eye-strain or psychomotor fatigue as compared with previous tests. The high sensitivity/variance relative to use in basic and applied research, and worksite fitness-for-duty testing, was discussed. The most distinct advantage of a software-based test that operates on readily available PCs is that it can be widely distributed to researchers with a common reference to compare a variety of alcohol and drug effects.

Internet Power Searching: The Advanced Manual. 2nd Edition. Neal-Schuman NetGuide Series.

ERIC Educational Resources Information Center

Bradley, Phil

This handbook provides information on how Internet search engines and related software and utilities work and how to use them in order to improve search techniques. The book begins with an introduction to the Internet. Part 1 contains the following chapters that cover mining the Internet for information: "An Introduction to Search…

Electronic Job Search Revolution. Win with the New Technology that's Reshaping Today's Job Market.

ERIC Educational Resources Information Center

Kennedy, Joyce Lain; Morrow, Thomas J.

This book contains information about the resources available to merge new technology and the search for employment. It offers suggestions from human resource specialists, software authors, and database experts. Chapter 1 is an overview of how the computer has become indispensable in a job search. Chapter 2 focuses on external, third-party resume…

Content analysis of cancer blog posts.

PubMed

Kim, Sujin

2009-10-01

The efficacy of user-defined subject tagging and software-generated subject tagging for describing and organizing cancer blog contents was explored. The Technorati search engine was used to search the blogosphere for cancer blog postings generated during a two-month period. Postings were mined for relevant subject concepts, and blogger-defined tags and Text Analysis Portal for Research (TAPoR) software-defined tags were generated for each message. Descriptive data were collected, and the blogger-defined tags were compared with software-generated tags. Three standard vocabularies (Opinion Templates, Basic Resource, and Medical Subject Headings [MeSH] Resource) were used to assign subject terms to the blogs, with results compared for efficacy in information retrieval. Descriptive data showed that most of the studied cancer blogs (80%) contained fewer than 500 words each. The numbers of blogger-defined tags per posting (M = 4.49 per posting) were significantly smaller than the TAPoR keywords (M = 23.55 per posting). Both blogger-defined subject tags and software-generated subject tags were often overly broad or overly narrow in focus, producing less than effective search results for those seeking to extract information from cancer blogs. Additional exploration into methods for systematically organizing cancer blog postings is necessary if blogs are to become stable and efficacious information resources for cancer patients, friends, families, or providers.

Future-saving audiovisual content for Data Science: Preservation of geoinformatics video heritage with the TIB|AV-Portal

NASA Astrophysics Data System (ADS)

Löwe, Peter; Plank, Margret; Ziedorn, Frauke

2015-04-01

In data driven research, the access to citation and preservation of the full triad consisting of journal article, research data and -software has started to become good scientific practice. To foster the adoption of this practice the significance of software tools has to be acknowledged, which enable scientists to harness auxiliary audiovisual content in their research work. The advent of ubiquitous computer-based audiovisual recording and corresponding Web 2.0 hosting platforms like Youtube, Slideshare and GitHub has created new ecosystems for contextual information related to scientific software and data, which continues to grow both in size and variety of content. The current Web 2.0 platforms lack capabilities for long term archiving and scientific citation, such as persistent identifiers allowing to reference specific intervals of the overall content. The audiovisual content currently shared by scientists ranges from commented howto-demonstrations on software handling, installation and data-processing, to aggregated visual analytics of the evolution of software projects over time. Such content are crucial additions to the scientific message, as they ensure that software-based data-processing workflows can be assessed, understood and reused in the future. In the context of data driven research, such content needs to be accessible by effective search capabilities, enabling the content to be retrieved and ensuring that the content producers receive credit for their efforts within the scientific community. Improved multimedia archiving and retrieval services for scientific audiovisual content which meet these requirements are currently implemented by the scientific library community. This paper exemplifies the existing challenges, requirements, benefits and the potential of the preservation, accessibility and citability of such audiovisual content for the Open Source communities based on the new audiovisual web service TIB|AV Portal of the German National Library of Science and Technology. The web-based portal allows for extended search capabilities based on enhanced metadata derived by automated video analysis. By combining state-of-the-art multimedia retrieval techniques such as speech-, text-, and image recognition with semantic analysis, content-based access to videos at the segment level is provided. Further, by using the open standard Media Fragment Identifier (MFID), a citable Digital Object Identifier is displayed for each video segment. In addition to the continuously growing footprint of contemporary content, the importance of vintage audiovisual information needs to be considered: This paper showcases the successful application of the TIB|AV-Portal in the preservation and provision of a newly discovered version of a GRASS GIS promotional video produced by US Army -Corps of Enginers Laboratory (US-CERL) in 1987. The video is provides insight into the constraints of the very early days of the GRASS GIS project, which is the oldest active Free and Open Source Software (FOSS) GIS project which has been active for over thirty years. GRASS itself has turned into a collaborative scientific platform and a repository of scientific peer-reviewed code and algorithm/knowledge hub for future generation of scientists [1]. This is a reference case for future preservation activities regarding semantic-enhanced Web 2.0 content from geospatial software projects within Academia and beyond. References: [1] Chemin, Y., Petras V., Petrasova, A., Landa, M., Gebbert, S., Zambelli, P., Neteler, M., Löwe, P.: GRASS GIS: a peer-reviewed scientific platform and future research Repository, Geophysical Research Abstracts, Vol. 17, EGU2015-8314-1, 2015 (submitted)

International Astronomical Search Collaboration: An Online Student-Based Discovery Program in Astronomy (Invited)

NASA Astrophysics Data System (ADS)

Pennypacker, C.; Miller, P.

2009-12-01

The past 15 years has seen the development of affordable small telescopes, advanced digital cameras, high speed Internet access, and widely-available image analysis software. With these tools it is possible to provide student programs where they make original astronomical discoveries. High school aged students, even younger, have discovered Main Belt asteroids (MBA), near-Earth objects (NEO), comets, supernovae, and Kuiper Belt objects (KBO). Student-based discovery is truly an innovative way to generate enthusiasm for learning science. The International Astronomical Search Collaboration (IASC = “Isaac”) is an online program where high school and college students make original MBA discoveries and important NEO observations. MBA discoveries are reported to the Minor Planet Center (Harvard) and International Astronomical Union. The NEO observations are included as part of the NASA Near-Earth Object Program (JPL). Provided at no cost to participating schools, IASC is centered at Hardin-Simmons University (Abilene, TX). It is a collaboration of the University, Lawrence Hall of Science (University of California, Berkeley), Astronomical Research Institute (ARI; Charleston, IL), Global Hands-On Universe Association (Portugal),and Astrometrica (Austria). Started in Fall 2006, IASC has reached 135 schools in 14 countries. There are 9 campaigns per year, each with 15 schools and lasting 45 days. Students have discovered 150 MBAs and made > 1,000 NEO observations. One notable discovery was 2009 BD81, discovered by two high school teachers and a graduate student at the Bulgarian Academy of Science. This object, about the size of 3 football fields, crosses Earth’s orbit and poses a serious impact risk. Each night with clear skies and no Moon, the ARI Observatory uses its 24" and 32" prime focus telescopes to take images along the ecliptic. Three images are taken of the same field of view (FOV) over a period of 30 minutes. These are bundled together and placed online at the IASC home site (iasc.hsutx.edu) into the participating school folders. In the morning, the students download their image sets, analyzing the set using the software Astrometrica. The software aligns the images using stars in the FOV then blinks them back and forth. The students easily see the asteroids moving in the background. Astrometrica records the times and celestial coordinates into a report that is forwarded to the Minor Planet Center. IASC is a volunteer-managed program. It has 17 volunteers from 6 countries. They run 9 campaigns per year for 135 schools, although the full capacity is 16 serving 240 schools world-wide. In addition to search campaigns open to any interested school, there have been dedicated campaigns including: 1) All-China Asteroid Search Campaign National Astronomical Observatory of China 2) All-Africa Asteroid Search Campaign South African Astronomical Observatory and Space School Africa 3) All-Texas Asteroid Search Campaign Texas Regional Collaboratives (University of Texas, Austin) Future plans for IASC include new campaigns searching for objects other than MBAs. These include comets, KBOs, supernovae, and active galactic nuclei. Students will also work on variable stars and asteroid light curves, and search for exoplanets.

RAPTOR: An Enterprise Knowledge Discovery Engine

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

2010-11-11

SharePoint search capability is commonly criticized by users due to the limited functionality provided. This software takes a world class search capability (Piranha) and integrates it with an Enterprise Level Collaboration Application installed on most major government and commercial sites.

NA-42 TI Shared Software Component Library FY2011 Final Report

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

Knudson, Christa K.; Rutz, Frederick C.; Dorow, Kevin E.

The NA-42 TI program initiated an effort in FY2010 to standardize its software development efforts with the long term goal of migrating toward a software management approach that will allow for the sharing and reuse of code developed within the TI program, improve integration, ensure a level of software documentation, and reduce development costs. The Pacific Northwest National Laboratory (PNNL) has been tasked with two activities that support this mission. PNNL has been tasked with the identification, selection, and implementation of a Shared Software Component Library. The intent of the library is to provide a common repository that is accessiblemore » by all authorized NA-42 software development teams. The repository facilitates software reuse through a searchable and easy to use web based interface. As software is submitted to the repository, the component registration process captures meta-data and provides version control for compiled libraries, documentation, and source code. This meta-data is then available for retrieval and review as part of library search results. In FY2010, PNNL and staff from the Remote Sensing Laboratory (RSL) teamed up to develop a software application with the goal of replacing the aging Aerial Measuring System (AMS). The application under development includes an Advanced Visualization and Integration of Data (AVID) framework and associated AMS modules. Throughout development, PNNL and RSL have utilized a common AMS code repository for collaborative code development. The AMS repository is hosted by PNNL, is restricted to the project development team, is accessed via two different geographic locations and continues to be used. The knowledge gained from the collaboration and hosting of this repository in conjunction with PNNL software development and systems engineering capabilities were used in the selection of a package to be used in the implementation of the software component library on behalf of NA-42 TI. The second task managed by PNNL is the development and continued maintenance of the NA-42 TI Software Development Questionnaire. This questionnaire is intended to help software development teams working under NA-42 TI in documenting their development activities. When sufficiently completed, the questionnaire illustrates that the software development activities recorded incorporate significant aspects of the software engineering lifecycle. The questionnaire template is updated as comments are received from NA-42 and/or its development teams and revised versions distributed to those using the questionnaire. PNNL also maintains a list of questionnaire recipients. The blank questionnaire template, the AVID and AMS software being developed, and the completed AVID AMS specific questionnaire are being used as the initial content to be established in the TI Component Library. This report summarizes the approach taken to identify requirements, search for and evaluate technologies, and the approach taken for installation of the software needed to host the component library. Additionally, it defines the process by which users request access for the contribution and retrieval of library content.« less

RadSearch: a RIS/PACS integrated query tool

NASA Astrophysics Data System (ADS)

Tsao, Sinchai; Documet, Jorge; Moin, Paymann; Wang, Kevin; Liu, Brent J.

2008-03-01

Radiology Information Systems (RIS) contain a wealth of information that can be used for research, education, and practice management. However, the sheer amount of information available makes querying specific data difficult and time consuming. Previous work has shown that a clinical RIS database and its RIS text reports can be extracted, duplicated and indexed for searches while complying with HIPAA and IRB requirements. This project's intent is to provide a software tool, the RadSearch Toolkit, to allow intelligent indexing and parsing of RIS reports for easy yet powerful searches. In addition, the project aims to seamlessly query and retrieve associated images from the Picture Archiving and Communication System (PACS) in situations where an integrated RIS/PACS is in place - even subselecting individual series, such as in an MRI study. RadSearch's application of simple text parsing techniques to index text-based radiology reports will allow the search engine to quickly return relevant results. This powerful combination will be useful in both private practice and academic settings; administrators can easily obtain complex practice management information such as referral patterns; researchers can conduct retrospective studies with specific, multiple criteria; teaching institutions can quickly and effectively create thorough teaching files.

Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching.

PubMed

Yates, John R

2015-11-01

Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures. Graphical Abstract ᅟ.

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

PubMed Central

2011-01-01

Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance. PMID:21631914

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

PubMed

Rognes, Torbjørn

2011-06-01

The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies.

PubMed

Milisavljevic, Marko; Hearty, Taryn; Wong, Tony Y T; Portales-Casamar, Elodie; Simpson, Elizabeth M; Wasserman, Wyeth W

2010-06-01

Laboratory Animal Management Assistant (LAMA) is an internet-based system for tracking large laboratory mouse colonies. It has a user-friendly interface with powerful search capabilities that ease day-to-day tasks such as tracking breeding cages and weaning litters. LAMA was originally developed to manage hundreds of new mouse strains generated by a large functional genomics program, the Pleiades Promoter Project ( http://www.pleiades.org ). The software system has proven to be highly flexible, suitable for diverse management approaches to mouse colonies. It allows custom tagging and grouping of animals, simplifying project-specific handling and access to data. Finally, LAMA was developed in close collaboration with mouse technicians to ease the transition from paper- or Excel-based management systems to computerized tracking, allowing data export in a popular spreadsheet format and automatic printing of cage cards. LAMA is an open-access software tool, freely available to the research community at http://launchpad.net/mousedb .

An ontology based information system for the management of institutional repository's collections

NASA Astrophysics Data System (ADS)

Tsolakidis, A.; Kakoulidis, P.; Skourlas, C.

2015-02-01

In this paper we discuss a simple methodological approach to create, and customize institutional repositories for the domain of the technological education. The use of the open source software platform of DSpace is proposed to build up the repository application and provide access to digital resources including research papers, dissertations, administrative documents, educational material, etc. Also the use of owl ontologies is proposed for indexing and accessing the various, heterogeneous items stored in the repository. Customization and operation of a platform for the selection and use of terms or parts of similar existing owl ontologies is also described. This platform could be based on the open source software Protégé that supports owl, is widely used, and also supports visualization, SPARQL etc. The combined use of the owl platform and the DSpace repository form a basis for creating customized ontologies, accommodating the semantic metadata of items and facilitating searching.

Survey of optimization techniques for nonlinear spacecraft trajectory searches

NASA Technical Reports Server (NTRS)

Wang, Tseng-Chan; Stanford, Richard H.; Sunseri, Richard F.; Breckheimer, Peter J.

1988-01-01

Mathematical analysis of the optimal search of a nonlinear spacecraft trajectory to arrive at a set of desired targets is presented. A high precision integrated trajectory program and several optimization software libraries are used to search for a converged nonlinear spacecraft trajectory. Several examples for the Galileo Jupiter Orbiter and the Ocean Topography Experiment (TOPEX) are presented that illustrate a variety of the optimization methods used in nonlinear spacecraft trajectory searches.

Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

PubMed

Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

2016-07-19

Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Analysis of CREW 3.1 System Center of Mass (COM)

DTIC Science & Technology

2010-09-01

reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection...5th percentile male values based on the 1988 U.S. Army Anthropometry Survey (ANSUR) (Gordon et al., 1989). Body weights were determined to be 216.21...also contains a utility for importing anthropometric data that is used to build and size the human figure models. This aspect of the software allows

New Technologies and the World Ahead: The Top 20 Plus 5

DTIC Science & Technology

2011-01-01

Specialized Agent Software Programs. Bots represent the next great milestone in soft- ware development. The general deployment of bots is projected to be in...knowledge and areas of interest. Powerful personal- agent 206 Moving from Vision to Action programs will search the Internet and its databases based on...language- capable chatbot and avatar interfaces that can control electronic data and also change and manipulate things in the physical world. These

COSMIC: Software catalog 1991 edition diskette format

NASA Technical Reports Server (NTRS)

1991-01-01

The PC edition of the annual COSMIC Software contains descriptions of the over 1,200 computer programs available for use within the United States as of January 1, 1991. By using the PC version of the catalog, it is possible to conduct extensive searches of the software inventory for programs that meet specific criteria. Elements such as program keywords, hardware specifications, source code languages, and title acronyms can be used for the basis of such searches. After isolating those programs that might be of best interest to the user, it is then possible to either view at the monitor, or generate a hardcopy listing of all information on those packages. In addition to the program elements that the user can search on, information such as total program size, distribution media, and program price, as well as extensive abstracts on the program, are also available to the user at this time. Another useful feature of the catalog allows for the retention of programs that meet certain search criteria between individual sessions of using the catalog. This allows users to save the information on those programs that are of interest to them in different areas of application. They can then recall a specific collection of programs for information retrieval or further search reduction if desired. In addition, this version of the catalog is adaptable to a network/shared resource environment, allowing multiple users access to a single copy of the catalog database simultaneously.

Agents, assemblers, and ANTS: scheduling assembly with market and biological software mechanisms

NASA Astrophysics Data System (ADS)

Toth-Fejel, Tihamer T.

2000-06-01

Nanoscale assemblers will need robust, scalable, flexible, and well-understood mechanisms such as software agents to control them. This paper discusses assemblers and agents, and proposes a taxonomy of their possible interaction. Molecular assembly is seen as a special case of general assembly, subject to many of the same issues, such as the advantages of convergent assembly, and the problem of scheduling. This paper discusses the contract net architecture of ANTS, an agent-based scheduling application under development. It also describes an algorithm for least commitment scheduling, which uses probabilistic committed capacity profiles of resources over time, along with realistic costs, to provide an abstract search space over which the agents can wander to quickly find optimal solutions.

Toward Evolvable Hardware Chips: Experiments with a Programmable Transistor Array

NASA Technical Reports Server (NTRS)

Stoica, Adrian

1998-01-01

Evolvable Hardware is reconfigurable hardware that self-configures under the control of an evolutionary algorithm. We search for a hardware configuration can be performed using software models or, faster and more accurate, directly in reconfigurable hardware. Several experiments have demonstrated the possibility to automatically synthesize both digital and analog circuits. The paper introduces an approach to automated synthesis of CMOS circuits, based on evolution on a Programmable Transistor Array (PTA). The approach is illustrated with a software experiment showing evolutionary synthesis of a circuit with a desired DC characteristic. A hardware implementation of a test PTA chip is then described, and the same evolutionary experiment is performed on the chip demonstrating circuit synthesis/self-configuration directly in hardware.

Training, Quality Assurance Factors, and Tools Investigation: a Work Report and Suggestions on Software Quality Assurance

NASA Technical Reports Server (NTRS)

Lee, Pen-Nan

1991-01-01

Previously, several research tasks have been conducted, some observations were obtained, and several possible suggestions have been contemplated involving software quality assurance engineering at NASA Johnson. These research tasks are briefly described. Also, a brief discussion is given on the role of software quality assurance in software engineering along with some observations and suggestions. A brief discussion on a training program for software quality assurance engineers is provided. A list of assurance factors as well as quality factors are also included. Finally, a process model which can be used for searching and collecting software quality assurance tools is presented.

Software Products - Naval Oceanography Portal

Science.gov Websites

section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You astronomy. Available as Fortran, C, or Python source code. Current version: 3.1 Software Products by Our computer or programmable calculator. Standards Of Fundamental Astronomy (SOFA) Libraries The International

[A survey on knowledge, attitude and practice related to evidence-based dentistry among dental students].

PubMed

Chang, Zhong-Fu; Zhu, Ce; Tao, Dan-Ying; Feng, Xi-Ping; Lu, Hai-Xia

2017-04-01

To investigate the knowledge, attitude and practice related to evidence-based dentistry among dental students, and to provide a reference for targeted evidence-based dentistry teaching and practice evidence-based dentistry in dental students. Dental students who attended the internship in Shanghai Ninth People's Hospital and Pudong People's Hospital were invited to attend this survey. Information on knowledge, attitude and practices related evidence-based dentistry was collected through questionnaires. SPSS 21.0 software package was used for data analysis. A total of 62 dental students attended this survey. Evidence-based dentistry related knowledge and attitude scores were 5.5±1.9 and 5.1±1.0, respectively. Over three quarters of students took courses on evidence-based medicine, while around half of students (56.5%) self-reported that they knew little about evidence-based medicine. 70.5% students practiced evidence-based dentistry less than once in the process of clinical decision making per week. The majority of students (80.3%) used MEDLINE or other databases to search for practice-related literature less than once per week. 63.9% students used practice guideline. The top three barriers to practice evidence-based dentistry were lack of information resources, insufficient time and lack of search skills. Evidence-based dentistry related knowledge and practice among dental students is deficient, whereas they hold positive attitude on practice. The top three barriers to practice evidence-based dentistry are lack of information resources, insufficient time and lack of search skills.

Is There a Standard Default Keyword Operator? A Bibliometric Analysis of Processing Options Chosen by Libraries To Execute Keyword Searches in Online Public Access Catalogs.

ERIC Educational Resources Information Center

Klein, Gary M.

1994-01-01

Online public access catalogs from 67 libraries using NOTIS software were searched using Internet connections to determine the positional operators selected as the default keyword operator on each catalog. Results indicate the lack of a processing standard for keyword searches. Five tables provide information. (Author/AEF)

Simulating a Direction-Finder Search for an ELT

NASA Technical Reports Server (NTRS)

Bream, Bruce

2005-01-01

A computer program simulates the operation of direction-finding equipment engaged in a search for an emergency locator transmitter (ELT) aboard an aircraft that has crashed. The simulated equipment is patterned after the equipment used by the Civil Air Patrol to search for missing aircraft. The program is designed to be used for training in radio direction-finding and/or searching for missing aircraft without incurring the expense and risk of using real aircraft and ground search resources. The program places a hidden ELT on a map and enables the user to search for the location of the ELT by moving a 14 NASA Tech Briefs, March 2005 small aircraft image around the map while observing signal-strength and direction readings on a simulated direction- finding locator instrument. As the simulated aircraft is turned and moved on the map, the program updates the readings on the direction-finding instrument to reflect the current position and heading of the aircraft relative to the location of the ELT. The software is distributed in a zip file that contains an installation program. The software runs on the Microsoft Windows 9x, NT, and XP operating systems.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

Methodology of problem-based learning engineering and technology and of its implementation with modern computer resources

NASA Astrophysics Data System (ADS)

Lebedev, A. A.; Ivanova, E. G.; Komleva, V. A.; Klokov, N. M.; Komlev, A. A.

2017-01-01

The considered method of learning the basics of microelectronic circuits and systems amplifier enables one to understand electrical processes deeper, to understand the relationship between static and dynamic characteristics and, finally, bring the learning process to the cognitive process. The scheme of problem-based learning can be represented by the following sequence of procedures: the contradiction is perceived and revealed; the cognitive motivation is provided by creating a problematic situation (the mental state of the student), moving the desire to solve the problem, to raise the question "why?", the hypothesis is made; searches for solutions are implemented; the answer is looked for. Due to the complexity of architectural schemes in the work the modern methods of computer analysis and synthesis are considered in the work. Examples of engineering by students in the framework of students' scientific and research work of analog circuits with improved performance based on standard software and software developed at the Department of Microelectronics MEPhI.

What Is the Proportion of Studies Reporting Patient and Practitioner Satisfaction with Software Support Tools Used in the Management of Knee Pain and Is This Related to Sample Size, Effect Size, and Journal Impact Factor?

PubMed

Bright, Philip; Hambly, Karen

2017-12-21

E-health software tools have been deployed in managing knee conditions. Reporting of patient and practitioner satisfaction in studies regarding e-health usage is not widely explored. The objective of this review was to identify studies describing patient and practitioner satisfaction with software use concerning knee pain. A computerized search was undertaken: four electronic databases were searched from January 2007 until January 2017. Key words were decision dashboard, clinical decision, Web-based resource, evidence support, and knee. Full texts were scanned for effect of size reporting and satisfaction scales from participants and practitioners. Binary regression was run; impact factor and sample size were predictors with indicators for satisfaction and effect size reporting as dependent variables. Seventy-seven articles were retrieved; 37 studies were included in final analysis. Ten studies reported patient satisfaction ratings (27.8%): a single study reported both patient and practitioner satisfaction (2.8%). Randomized control trials were the most common design (35%) and knee osteoarthritis the most prevalent condition (38%). Electronic patient-reported outcome measures and Web-based training were the most common interventions. No significant dependency was found within the regression models (p > 0.05). The proportion of reporting of patient satisfaction was low; practitioner satisfaction was poorly represented. There may be implications for the suitability of administering e-health, a medium for capturing further meta-evidence needs to be established and used as best practice for implicated studies in future. This is the first review of its kind to address patient and practitioner satisfaction with knee e-health.

Search for extraterrestrial intelligence/High Resolution Microwave Survey team member

NASA Technical Reports Server (NTRS)

Steffes, Paul G.

1994-01-01

This final report summarizes activities conducted during the three years of the NASA High Resolution Microwave Survey (HRMS). With primary interest in the Sky Survey activity, the principal investigator attended nine Working Group meetings and traveled independently to conduct experiments or present results at other meetings. The major activity involved evaluating the effects of spaceborne radio frequency interference (RFI) on both the SETI sky survey and targeted search. The development of a database of all unclassified earth or biting and deep space transmitters, along with accompanying search software, was a key accomplishment. The software provides information about potential sources of interference and gives complete information regarding the frequencies, positions and levels of interference generated by the spacecraft. A complete description of this search system (called HRS, or HRMS RFI Search) is provided. Other accomplishments include development of a 32,000 channel Fast-Fourier-Transform Spectrum analyzer for use in studies of interference from satellites and in a 1.4 mm SETI observational study. The latest revision of HRS has now been distributed to the extended radio astronomy and SETI community.

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

DOE PAGES

Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

2013-03-07

In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

LandEx - Fast, FOSS-Based Application for Query and Retrieval of Land Cover Patterns

NASA Astrophysics Data System (ADS)

Netzel, P.; Stepinski, T.

2012-12-01

The amount of satellite-based spatial data is continuously increasing making a development of efficient data search tools a priority. The bulk of existing research on searching satellite-gathered data concentrates on images and is based on the concept of Content-Based Image Retrieval (CBIR); however, available solutions are not efficient and robust enough to be put to use as deployable web-based search tools. Here we report on development of a practical, deployable tool that searches classified, rather than raw image. LandEx (Landscape Explorer) is a GeoWeb-based tool for Content-Based Pattern Retrieval (CBPR) contained within the National Land Cover Dataset 2006 (NLCD2006). The USGS-developed NLCD2006 is derived from Landsat multispectral images; it covers the entire conterminous U.S. with the resolution of 30 meters/pixel and it depicts 16 land cover classes. The size of NLCD2006 is about 10 Gpixels (161,000 x 100,000 pixels). LandEx is a multi-tier GeoWeb application based on Open Source Software. Main components are: GeoExt/OpenLayers (user interface), GeoServer (OGC WMS, WCS and WPS server), and GRASS (calculation engine). LandEx performs search using query-by-example approach: user selects a reference scene (exhibiting a chosen pattern of land cover classes) and the tool produces, in real time, a map indicating a degree of similarity between the reference pattern and all local patterns across the U.S. Scene pattern is encapsulated by a 2D histogram of classes and sizes of single-class clumps. Pattern similarity is based on the notion of mutual information. The resultant similarity map can be viewed and navigated in a web browser, or it can download as a GeoTiff file for more in-depth analysis. The LandEx is available at http://sil.uc.edu

LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

PubMed

Zhang, Wei; Zhang, Jiyang; Xu, Changming; Li, Ning; Liu, Hui; Ma, Jie; Zhu, Yunping; Xie, Hongwei

2012-12-01

Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Concentrations of indoor pollutants database: User's manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Concentrations of indoor pollutants database: User`s manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Development of a Google-based search engine for data mining radiology reports.

PubMed

Erinjeri, Joseph P; Picus, Daniel; Prior, Fred W; Rubin, David A; Koppel, Paul

2009-08-01

The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google's XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like "pneumothorax" yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like "hemangioendothelioma" yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google's interface, radiologists can quickly perform useful searches.

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

Trabant, C.; Reyes, C. G.; Clark, A.; Karstens, R.

2012-12-01

SeisCode is a community repository for software used in seismological and related fields. The repository is intended to increase discoverability of such software and to provide a long-term home for software projects. Other places exist where seismological software may be found, but none meet the requirements necessary for an always current, easy to search, well documented, and citable resource for projects. Organizations such as IRIS, ORFEUS, and the USGS have websites with lists of available or contributed seismological software. Since the authors themselves do often not maintain these lists, the documentation often consists of a sentence or paragraph, and the available software may be outdated. Repositories such as GoogleCode and SourceForge, which are directly maintained by the authors, provide version control and issue tracking but do not provide a unified way of locating geophysical software scattered in and among countless unrelated projects. Additionally, projects are hosted at language-specific sites such as Mathworks and PyPI, in FTP directories, and in websites strewn across the Web. Search engines are only partially effective discovery tools, as the desired software is often hidden deep within the results. SeisCode provides software authors a place to present their software, codes, scripts, tutorials, and examples to the seismological community. Authors can choose their own level of involvement. At one end of the spectrum, the author might simply create a web page that points to an existing site. At the other extreme, an author may choose to leverage the many tools provided by SeisCode, such as a source code management tool with integrated issue tracking, forums, news feeds, downloads, wikis, and more. For software development projects with multiple authors, SeisCode can also be used as a central site for collaboration. SeisCode provides the community with an easy way to discover software, while providing authors a way to build a community around their software packages. IRIS invites the seismological community to browse and to submit projects to https://seiscode.iris.washington.edu/

Front End Software for Online Database Searching. Part 2: The Marketplace.

ERIC Educational Resources Information Center

Levy, Louise R.; Hawkins, Donald T.

1986-01-01

This article analyzes the front end software marketplace and discusses some of the complex forces influencing it. Discussion covers intermediary market; end users (library customers, scientific and technical professionals, corporate business specialists, consumers); marketing strategies; a British front end development firm; competitive pressures;…

Integrating Ideas for International Data Collaborations Through The Committee on Earth Observation Satellites (CEOS) International Directory Network (IDN)

NASA Technical Reports Server (NTRS)

Olsen, Lola M.

2006-01-01

The capabilities of the International Directory Network's (IDN) version MD9.5, along with a new version of the metadata authoring tool, "docBUILDER", will be presented during the Technology and Services Subgroup session of the Working Group on Information Systems and Services (WGISS). Feedback provided through the international community has proven instrumental in positively influencing the direction of the IDN s development. The international community was instrumental in encouraging support for using the IS0 international character set that is now available through the directory. Supporting metadata descriptions in additional languages encourages extended use of the IDN. Temporal and spatial attributes often prove pivotal in the search for data. Prior to the new software release, the IDN s geospatial and temporal searches suffered from browser incompatibilities and often resulted in unreliable performance for users attempting to initiate a spatial search using a map based on aging Java applet technology. The IDN now offers an integrated Google map and date search that replaces that technology. In addition, one of the most defining characteristics in the search for data relates to the temporal and spatial resolution of the data. The ability to refine the search for data sets meeting defined resolution requirements is now possible. Data set authors are encouraged to indicate the precise resolution values for their data sets and subsequently bin these into one of the pre-selected resolution ranges. New metadata authoring tools have been well received. In response to requests for a standalone metadata authoring tool, a new shareable software package called "docBUILDER solo" will soon be released to the public. This tool permits researchers to document their data during experiments and observational periods in the field. interoperability has been enhanced through the use of the Open Archives Initiative s (OAI) Protocol for Metadata Harvesting (PMH). Harvesting of XML content through OAI-MPH has been successfully tested with several organizations. The protocol appears to be a prime candidate for sharing metadata throughout the international community. Data services for visualizing and analyzing data have become valuable assets in facilitating the use of data. Data providers are offering many of their data-related services through the directory. The IDN plans to develop a service-based architecture to further promote the use of web services. During the IDN Task Team session, ideas for further enhancements will be discussed.

PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms.

PubMed

Meereis, Florian; Kaufmann, Michael

2004-10-15

The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (COGs). There are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for COGs containing (almost) exclusively proteins from (hyper)thermophilic genomes. However, public software to perform individually definable group-specific searches is not available. The tool described here exactly fills this gap. The software is accessible at http://www.uni-wh.de/pcogr and is linked to the COG-database. The user can freely define two groups of organisms by selecting for each of the (current) 66 organisms to belong either to groupA, to the reference groupB or to be ignored by the algorithm. Then, for all COGs a specificity index is calculated with respect to the specificity to groupA, i. e. high scoring COGs contain proteins from the most of groupA organisms while proteins from the most organisms assigned to groupB are absent. In addition to ranking all COGs according to the user defined specificity criteria, a graphical visualization shows the distribution of all COGs by displaying their abundance as a function of their specificity indexes. This software allows detecting COGs specific to a predefined group of organisms. All COGs are ranked in the order of their specificity and a graphical visualization allows recognizing (i) the presence and abundance of such COGs and (ii) the phylogenetic relationship between groupA- and groupB-organisms. The software also allows detecting putative protein-protein interactions, novel enzymes involved in only partially known biochemical pathways, and alternate enzymes originated by convergent evolution.

Domain similarity based orthology detection.

PubMed

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-05-13

Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

Using Selection Pressure as an Asset to Develop Reusable, Adaptable Software Systems

NASA Astrophysics Data System (ADS)

Berrick, S. W.; Lynnes, C.

2007-12-01

The Goddard Earth Sciences Data and Information Services Center (GES DISC) at NASA has over the years developed and honed a number of reusable architectural components for supporting large-scale data centers with a large customer base. These include a processing system (S4PM) and an archive system (S4PA) based upon a workflow engine called the Simple, Scalable, Script-based Science Processor (S4P); an online data visualization and analysis system (Giovanni); and the radically simple and fast data search tool, Mirador. These subsystems are currently reused internally in a variety of combinations to implement customized data management on behalf of instrument science teams and other science investigators. Some of these subsystems (S4P and S4PM) have also been reused by other data centers for operational science processing. Our experience has been that development and utilization of robust, interoperable, and reusable software systems can actually flourish in environments defined by heterogeneous commodity hardware systems, the emphasis on value-added customer service, and continual cost reduction pressures. The repeated internal reuse that is fostered by such an environment encourages and even forces changes to the software that make it more reusable and adaptable. Allowing and even encouraging such selective pressures to software development has been a key factor in the success of S4P and S4PM, which are now available to the open source community under the NASA Open Source Agreement.

A CCD search of short period variable stars in six selected fields. (Italian Title: Ricerca CCD di variabili a breve periodo in sei campi selezionati)

NASA Astrophysics Data System (ADS)

Valentini, S.

2013-12-01

A search of variable stars was carried out, using a new software specifically created by the author, on a series of images acquired at the Astronomical Observatory of Santa Lucia di Stroncone (Terni, Italy) between October 2010 and March 2012. This research, named Fast Variable Stars Survey (FVSS), arose from the idea to verify if the log files pr oduced by the software Astrometrica (H. Raab), could be used as a basis for rapid detection of short-period variable stars. The r esults obtained showed that the idea is very valid, so that the new software has allowed the identification and the correct determination of the period of thirty-two new variable stars in the six stellar fields subjected to analysis.

Hybrid Optimization Parallel Search PACKage

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

2009-11-10

HOPSPACK is open source software for solving optimization problems without derivatives. Application problems may have a fully nonlinear objective function, bound constraints, and linear and nonlinear constraints. Problem variables may be continuous, integer-valued, or a mixture of both. The software provides a framework that supports any derivative-free type of solver algorithm. Through the framework, solvers request parallel function evaluation, which may use MPI (multiple machines) or multithreading (multiple processors/cores on one machine). The framework provides a Cache and Pending Cache of saved evaluations that reduces execution time and facilitates restarts. Solvers can dynamically create other algorithms to solve subproblems, amore » useful technique for handling multiple start points and integer-valued variables. HOPSPACK ships with the Generating Set Search (GSS) algorithm, developed at Sandia as part of the APPSPACK open source software project.« less

All Source Sensor Analysis

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

- PNNL, Harold Trease

2012-10-10

ASSA is a software application that processes binary data into summarized index tables that can be used to organize features contained within the data. ASSA's index tables can also be used to search for user specified features. ASSA is designed to organize and search for patterns in unstructured binary data streams or archives, such as video, images, audio, and network traffic. ASSA is basically a very general search engine used to search for any pattern in any binary data stream. It has uses in video analytics, image analysis, audio analysis, searching hard-drives, monitoring network traffic, etc.

Autonomous Cryogenic Load Operations: Knowledge-Based Autonomous Test Engineer

NASA Technical Reports Server (NTRS)

Schrading, J. Nicolas

2013-01-01

The Knowledge-Based Autonomous Test Engineer (KATE) program has a long history at KSC. Now a part of the Autonomous Cryogenic Load Operations (ACLO) mission, this software system has been sporadically developed over the past 20 years. Originally designed to provide health and status monitoring for a simple water-based fluid system, it was proven to be a capable autonomous test engineer for determining sources of failure in the system. As part of a new goal to provide this same anomaly-detection capability for a complicated cryogenic fluid system, software engineers, physicists, interns and KATE experts are working to upgrade the software capabilities and graphical user interface. Much progress was made during this effort to improve KATE. A display of the entire cryogenic system's graph, with nodes for components and edges for their connections, was added to the KATE software. A searching functionality was added to the new graph display, so that users could easily center their screen on specific components. The GUI was also modified so that it displayed information relevant to the new project goals. In addition, work began on adding new pneumatic and electronic subsystems into the KATE knowledge base, so that it could provide health and status monitoring for those systems. Finally, many fixes for bugs, memory leaks, and memory errors were implemented and the system was moved into a state in which it could be presented to stakeholders. Overall, the KATE system was improved and necessary additional features were added so that a presentation of the program and its functionality in the next few months would be a success.

A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

PubMed

Salem, Rany M; Wessel, Jennifer; Schork, Nicholas J

2005-03-01

Interest in the assignment and frequency analysis of haplotypes in samples of unrelated individuals has increased immeasurably as a result of the emphasis placed on haplotype analyses by, for example, the International HapMap Project and related initiatives. Although there are many available computer programs for haplotype analysis applicable to samples of unrelated individuals, many of these programs have limitations and/or very specific uses. In this paper, the key features of available haplotype analysis software for use with unrelated individuals, as well as pooled DNA samples from unrelated individuals, are summarised. Programs for haplotype analysis were identified through keyword searches on PUBMED and various internet search engines, a review of citations from retrieved papers and personal communications, up to June 2004. Priority was given to functioning computer programs, rather than theoretical models and methods. The available software was considered in light of a number of factors: the algorithm(s) used, algorithm accuracy, assumptions, the accommodation of genotyping error, implementation of hypothesis testing, handling of missing data, software characteristics and web-based implementations. Review papers comparing specific methods and programs are also summarised. Forty-six haplotyping programs were identified and reviewed. The programs were divided into two groups: those designed for individual genotype data (a total of 43 programs) and those designed for use with pooled DNA samples (a total of three programs). The accuracy of programs using various criteria are assessed and the programs are categorised and discussed in light of: algorithm and method, accuracy, assumptions, genotyping error, hypothesis testing, missing data, software characteristics and web implementation. Many available programs have limitations (eg some cannot accommodate missing data) and/or are designed with specific tasks in mind (eg estimating haplotype frequencies rather than assigning most likely haplotypes to individuals). It is concluded that the selection of an appropriate haplotyping program for analysis purposes should be guided by what is known about the accuracy of estimation, as well as by the limitations and assumptions built into a program.

cluster trials v. 1.0

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

Mitchell, John; Castillo, Andrew

2016-09-21

This software contains a set of python modules – input, search, cluster, analysis; these modules read input files containing spatial coordinates and associated attributes which can be used to perform nearest neighbor search (spatial indexing via kdtree), cluster analysis/identification, and calculation of spatial statistics for analysis.

Integrating Query of Relational and Textual Data in Clinical Databases: A Case Study

PubMed Central

Fisk, John M.; Mutalik, Pradeep; Levin, Forrest W.; Erdos, Joseph; Taylor, Caroline; Nadkarni, Prakash

2003-01-01

Objectives: The authors designed and implemented a clinical data mart composed of an integrated information retrieval (IR) and relational database management system (RDBMS). Design: Using commodity software, which supports interactive, attribute-centric text and relational searches, the mart houses 2.8 million documents that span a five-year period and supports basic IR features such as Boolean searches, stemming, and proximity and fuzzy searching. Measurements: Results are relevance-ranked using either “total documents per patient” or “report type weighting.” Results: Non-curated medical text has a significant degree of malformation with respect to spelling and punctuation, which creates difficulties for text indexing and searching. Presently, the IR facilities of RDBMS packages lack the features necessary to handle such malformed text adequately. Conclusion: A robust IR+RDBMS system can be developed, but it requires integrating RDBMSs with third-party IR software. RDBMS vendors need to make their IR offerings more accessible to non-programmers. PMID:12509355

The Virtual Solar Observatory and the Heliophysics Meta-Virtual Observatory

NASA Technical Reports Server (NTRS)

Gurman, Joseph B.

2007-01-01

The Virtual Solar Observatory (VSO) is now able to search for solar data ranging from the radio to gamma rays, obtained from space and groundbased observatories, from 26 sources at 12 data providers, and from 1915 to the present. The solar physics community can use a Web interface or an Application Programming Interface (API) that allows integrating VSO searches into other software, including other Web services. Over the next few years, this integration will be especially obvious as the NASA Heliophysics division sponsors the development of a heliophysics-wide virtual observatory (VO), based on existing VO's in heliospheric, magnetospheric, and ionospheric physics as well as the VSO. We examine some of the challenges and potential of such a "meta-VO."

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

PubMed Central

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2016-01-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

PubMed

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

NASA Astrophysics Data System (ADS)

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

Scene Analysis: Non-Linear Spatial Filtering for Automatic Target Detection.

DTIC Science & Technology

1982-12-01

In this thesis, a method for two-dimensional pattern recognition was developed and tested. The method included a global search scheme for candidate...test global switch TYPEO Creating negative video file only.W 11=0 12=256 13=512 14=768 GO 70 2 1 TYPE" Creating negative and horizontally flipped video...purpose was to develop a base of image processing software for the AFIT Digital Signal Processing Laboratory NOVA- ECLIPSE minicomputer system, for

An information gathering system for medical image inspection

NASA Astrophysics Data System (ADS)

Lee, Young-Jin; Bajcsy, Peter

2005-04-01

We present an information gathering system for medical image inspection that consists of software tools for capturing computer-centric and human-centric information. Computer-centric information includes (1) static annotations, such as (a) image drawings enclosing any selected area, a set of areas with similar colors, a set of salient points, and (b) textual descriptions associated with either image drawings or links between pairs of image drawings, and (2) dynamic (or temporal) information, such as mouse movements, zoom level changes, image panning and frame selections from an image stack. Human-centric information is represented by video and audio signals that are acquired by computer-mounted cameras and microphones. The short-term goal of the presented system is to facilitate learning of medical novices from medical experts, while the long-term goal is to data mine all information about image inspection for assisting in making diagnoses. In this work, we built basic software functionality for gathering computer-centric and human-centric information of the aforementioned variables. Next, we developed the information playback capabilities of all gathered information for educational purposes. Finally, we prototyped text-based and image template-based search engines to retrieve information from recorded annotations, for example, (a) find all annotations containing the word "blood vessels", or (b) search for similar areas to a selected image area. The information gathering system for medical image inspection reported here has been tested with images from the Histology Atlas database.

Problem Solving Software for Math Classes.

ERIC Educational Resources Information Center

Troutner, Joanne

1987-01-01

Described are 10 computer software programs for problem solving related to mathematics. Programs described are: (1) Box Solves Story Problems; (2) Safari Search; (3) Puzzle Tanks; (4) The King's Rule; (5) The Factory; (6) The Royal Rules; (7) The Enchanted Forest; (8) Gears; (9) The Super Factory; and (10) Creativity Unlimited. (RH)

Bibliographic Management Software Seminars: Funding and Implementation.

ERIC Educational Resources Information Center

Henry, Marcia

This paper contains the grant proposal and final report for a project conducted by the California State University at Northridge library to demonstrate online database searching and introduce the use of bibliographic management software to faculty and graduate students. Day-long, discipline-oriented seminars were planned to increase the…

SABRE--A Novel Software Tool for Bibliographic Post-Processing.

ERIC Educational Resources Information Center

Burge, Cecil D.

1989-01-01

Describes the software architecture and application of SABRE (Semi-Automated Bibliographic Environment), which is one of the first products to provide a semi-automatic environment for relevancy ranking of citations obtained from searches of bibliographic databases. Features designed to meet the review, categorization, culling, and reporting needs…

wbstats

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

Piburn, Jesse

2016-04-22

Availability of accessing the World Bank Data API through the R language was limited to one existing package, which is limited in its ability. The software provides access to all of the features in World Bank API in one software package for the R language and provides functions for searching and downloading data from the World Bank API.

Development of a tool for documenting, tracking, recording, and analyzing improvements to intersection sites and roadway departures in curve locations.

DOT National Transportation Integrated Search

2015-04-01

The principal objectives and scope of this project were to provide a software tracking tool to improve : decision-making for highway safety. A literature search revealed that purchasing and customizing : existing software was not feasible and a new s...

Moving Object Detection Using a Parallax Shift Vector Algorithm

NASA Astrophysics Data System (ADS)

Gural, Peter S.; Otto, Paul R.; Tedesco, Edward F.

2018-07-01

There are various algorithms currently in use to detect asteroids from ground-based observatories, but they are generally restricted to linear or mildly curved movement of the target object across the field of view. Space-based sensors in high inclination, low Earth orbits can induce significant parallax in a collected sequence of images, especially for objects at the typical distances of asteroids in the inner solar system. This results in a highly nonlinear motion pattern of the asteroid across the sensor, which requires a more sophisticated search pattern for detection processing. Both the classical pattern matching used in ground-based asteroid search and the more sensitive matched filtering and synthetic tracking techniques, can be adapted to account for highly complex parallax motion. A new shift vector generation methodology is discussed along with its impacts on commonly used detection algorithms, processing load, and responsiveness to asteroid track reporting. The matched filter, template generator, and pattern matcher source code for the software described herein are available via GitHub.

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

PubMed Central

Chen, Ming; Henry, Nathan; Almsaeed, Abdullah; Zhou, Xiao; Wegrzyn, Jill; Ficklin, Stephen

2017-01-01

Abstract Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression PMID:29220446

Vocabulary Control and the Humanities: A Case Study of the "MLA International Bibliography."

ERIC Educational Resources Information Center

Stebelman, Scott

1994-01-01

Discussion of research in the humanities focuses on the "MLA International Bibliography," the primary database for literary research. Highlights include comparisons to research in the sciences; humanities vocabulary; database search techniques; contextual indexing; examples of searches; thesauri; and software. (43 references) (LRW)

Search without Boundaries Using Simple APIs

ERIC Educational Resources Information Center

Tong, Qi (Helen)

2009-01-01

The U.S. Geological Survey (USGS) Library, where the author serves as the digital services librarian, is increasingly challenged to make it easier for users to find information from many heterogeneous information sources. Information is scattered throughout different software applications (i.e., library catalog, federated search engine, link…

NEOview: Near Earth Object Data Discovery and Query

NASA Astrophysics Data System (ADS)

Tibbetts, M.; Elvis, M.; Galache, J. L.; Harbo, P.; McDowell, J. C.; Rudenko, M.; Van Stone, D.; Zografou, P.

2013-10-01

Missions to Near Earth Objects (NEOs) figure prominently in NASA's Flexible Path approach to human space exploration. NEOs offer insight into both the origins of the Solar System and of life, as well as a source of materials for future missions. With NEOview scientists can locate NEO datasets, explore metadata provided by the archives, and query or combine disparate NEO datasets in the search for NEO candidates for exploration. NEOview is a software system that illustrates how standards-based interfaces facilitate NEO data discovery and research. NEOview software follows a client-server architecture. The server is a configurable implementation of the International Virtual Observatory Alliance (IVOA) Table Access Protocol (TAP), a general interface for tabular data access, that can be deployed as a front end to existing NEO datasets. The TAP client, seleste, is a graphical interface that provides intuitive means of discovering NEO providers, exploring dataset metadata to identify fields of interest, and constructing queries to retrieve or combine data. It features a powerful, graphical query builder capable of easing the user's introduction to table searches. Through science use cases, NEOview demonstrates how potential targets for NEO rendezvous could be identified by combining data from complementary sources. Through deployment and operations, it has been shown that the software components are data independent and configurable to many different data servers. As such, NEOview's TAP server and seleste TAP client can be used to create a seamless environment for data discovery and exploration for tabular data in any astronomical archive.

Kepler: A Search for Terrestrial Planets - SOC 9.3 DR25 Pipeline Parameter Configuration Reports

NASA Technical Reports Server (NTRS)

Campbell, Jennifer R.

2017-01-01

This document describes the manner in which the pipeline and algorithm parameters for the Kepler Science Operations Center (SOC) science data processing pipeline were managed. This document is intended for scientists and software developers who wish to better understand the software design for the final Kepler codebase (SOC 9.3) and the effect of the software parameters on the Data Release (DR) 25 archival products.

Automation and hypermedia technology applications

NASA Technical Reports Server (NTRS)

Jupin, Joseph H.; Ng, Edward W.; James, Mark L.

1993-01-01

This paper represents a progress report on HyLite (Hypermedia Library technology): a research and development activity to produce a versatile system as part of NASA's technology thrusts in automation, information sciences, and communications. HyLite can be used as a system or tool to facilitate the creation and maintenance of large distributed electronic libraries. The contents of such a library may be software components, hardware parts or designs, scientific data sets or databases, configuration management information, etc. Proliferation of computer use has made the diversity and quantity of information too large for any single user to sort, process, and utilize effectively. In response to this information deluge, we have created HyLite to enable the user to process relevant information into a more efficient organization for presentation, retrieval, and readability. To accomplish this end, we have incorporated various AI techniques into the HyLite hypermedia engine to facilitate parameters and properties of the system. The proposed techniques include intelligent searching tools for the libraries, intelligent retrievals, and navigational assistance based on user histories. HyLite itself is based on an earlier project, the Encyclopedia of Software Components (ESC) which used hypermedia to facilitate and encourage software reuse.

Automatic relative RPC image model bias compensation through hierarchical image matching for improving DEM quality

NASA Astrophysics Data System (ADS)

Noh, Myoung-Jong; Howat, Ian M.

2018-02-01

The quality and efficiency of automated Digital Elevation Model (DEM) extraction from stereoscopic satellite imagery is critically dependent on the accuracy of the sensor model used for co-locating pixels between stereo-pair images. In the absence of ground control or manual tie point selection, errors in the sensor models must be compensated with increased matching search-spaces, increasing both the computation time and the likelihood of spurious matches. Here we present an algorithm for automatically determining and compensating the relative bias in Rational Polynomial Coefficients (RPCs) between stereo-pairs utilizing hierarchical, sub-pixel image matching in object space. We demonstrate the algorithm using a suite of image stereo-pairs from multiple satellites over a range stereo-photogrammetrically challenging polar terrains. Besides providing a validation of the effectiveness of the algorithm for improving DEM quality, experiments with prescribed sensor model errors yield insight into the dependence of DEM characteristics and quality on relative sensor model bias. This algorithm is included in the Surface Extraction through TIN-based Search-space Minimization (SETSM) DEM extraction software package, which is the primary software used for the U.S. National Science Foundation ArcticDEM and Reference Elevation Model of Antarctica (REMA) products.

Lessons learned from a pilot implementation of the UMLS information sources map.

PubMed

Miller, P L; Frawley, S J; Wright, L; Roderer, N K; Powsner, S M

1995-01-01

To explore the software design issues involved in implementing an operational information sources map (ISM) knowledge base (KB) and system of navigational tools that can help medical users access network-based information sources relevant to a biomedical question. A pilot biomedical ISM KB and associated client-server software (ISM/Explorer) have been developed to help students, clinicians, researchers, and staff access network-based information sources, as part of the National Library of Medicine's (NLM) multi-institutional Unified Medical Language System (UMLS) project. The system allows the user to specify and constrain a search for a biomedical question of interest. The system then returns a list of sources matching the search. At this point the user may request 1) further information about a source, 2) that the list of sources be regrouped by different criteria to allow the user to get a better overall appreciation of the set of retrieved sources as a whole, or 3) automatic connection to a source. The pilot system operates in client-server mode and currently contains coded information for 121 sources. It is in routine use from approximately 40 workstations at the Yale School of Medicine. The lessons that have been learned are that: 1) it is important to make access to different versions of a source as seamless as possible, 2) achieving seamless, cross-platform access to heterogeneous sources is difficult, 3) significant differences exist between coding the subject content of an electronic information resource versus that of an article or a book, 4) customizing the ISM to multiple institutions entails significant complexities, and 5) there are many design trade-offs between specifying searches and viewing sets of retrieved sources that must be taken into consideration. An ISM KB and navigational tools have been constructed. In the process, much has been learned about the complexities of development and evaluation in this new environment, which are different from those for Gopher, wide area information servers (WAIS), World-Wide-Web (WWW), and MOSAIC resources.

Web catalog of oceanographic data using GeoNetwork

NASA Astrophysics Data System (ADS)

Marinova, Veselka; Stefanov, Asen

2017-04-01

Most of the data collected, analyzed and used by Bulgarian oceanographic data center (BgODC) from scientific cruises, argo floats, ferry boxes and real time operating systems are spatially oriented and need to be displayed on the map. The challenge is to make spatial information more accessible to users, decision makers and scientists. In order to meet this challenge, BgODC concentrate its efforts on improving dynamic and standardized access to their geospatial data as well as those from various related organizations and institutions. BgODC currently is implementing a project to create a geospatial portal for distributing metadata and search, exchange and harvesting spatial data. There are many open source software solutions able to create such spatial data infrastructure (SDI). Finally, the GeoNetwork open source is chosen, as it is already widespread. This software is free, effective and "cheap" solution for implementing SDI at organization level. It is platform independent and runs under many operating systems. Filling of the catalog goes through these practical steps: • Managing and storing data reliably within MS SQL spatial data base; • Registration of maps and data of various formats and sources in GeoServer (most popular open source geospatial server embedded with GeoNetwork) ; • Filling added meta data and publishing geospatial data at the desktop of GeoNetwork. GeoServer and GeoNetwork are based on Java so they require installing of a servlet engine like Tomcat. The experience gained from the use of GeoNetwork Open Source confirms that the catalog meets the requirements for data management and is flexible enough to customize. Building the catalog facilitates sustainable data exchange between end users. The catalog is a big step towards implementation of the INSPIRE directive due to availability of many features necessary for producing "INSPIRE compliant" metadata records. The catalog now contains all available GIS data provided by BgODC for Internet access. Searching data within the catalog is based upon geographic extent, theme type and free text search.

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

Determination of Slope Safety Factor with Analytical Solution and Searching Critical Slip Surface with Genetic-Traversal Random Method

PubMed Central

2014-01-01

In the current practice, to determine the safety factor of a slope with two-dimensional circular potential failure surface, one of the searching methods for the critical slip surface is Genetic Algorithm (GA), while the method to calculate the slope safety factor is Fellenius' slices method. However GA needs to be validated with more numeric tests, while Fellenius' slices method is just an approximate method like finite element method. This paper proposed a new method to determine the minimum slope safety factor which is the determination of slope safety factor with analytical solution and searching critical slip surface with Genetic-Traversal Random Method. The analytical solution is more accurate than Fellenius' slices method. The Genetic-Traversal Random Method uses random pick to utilize mutation. A computer automatic search program is developed for the Genetic-Traversal Random Method. After comparison with other methods like slope/w software, results indicate that the Genetic-Traversal Random Search Method can give very low safety factor which is about half of the other methods. However the obtained minimum safety factor with Genetic-Traversal Random Search Method is very close to the lower bound solutions of slope safety factor given by the Ansys software. PMID:24782679

Managing Content in a Matter of Minutes

NASA Technical Reports Server (NTRS)

2004-01-01

NASA software created to help scientists expeditiously search and organize their research documents is now aiding compliance personnel, law enforcement investigators, and the general public in their efforts to search, store, manage, and retrieve documents more efficiently. Developed at Ames Research Center, NETMARK software was designed to manipulate vast amounts of unstructured and semi-structured NASA documents. NETMARK is both a relational and object-oriented technology built on an Oracle enterprise-wide database. To ensure easy user access, Ames constructed NETMARK as a Web-enabled platform utilizing the latest in Internet technology. One of the significant benefits of the program was its ability to store and manage mission-critical data.

Administrative Issues in Planning a Library End User Searching Program. ERIC Digest.

ERIC Educational Resources Information Center

Machovec, George S.

This digest presents a reprint of an article which examines management principles that should be considered when implementing library end user searching programs. A brief discussion of specific implementation issues includes needs assessment, hardware, software, training, budgeting, what systems to offer, publicity and marketing, policies and…

Internet Technology--Going beyond Google

ERIC Educational Resources Information Center

Warger, Tom

2006-01-01

Over the past dozen years, the switch from paper to electronic sources of information has been all encompassing. How can technology support the efforts of scholars to find and evaluate information? General-purpose search engines use an obscure mix of advanced algorithms to index, search, match, and rank results. Metasearch software extends the…

[Development of domain specific search engines].

PubMed

Takai, T; Tokunaga, M; Maeda, K; Kaminuma, T

2000-01-01

As cyber space exploding in a pace that nobody has ever imagined, it becomes very important to search cyber space efficiently and effectively. One solution to this problem is search engines. Already a lot of commercial search engines have been put on the market. However these search engines respond with such cumbersome results that domain specific experts can not tolerate. Using a dedicate hardware and a commercial software called OpenText, we have tried to develop several domain specific search engines. These engines are for our institute's Web contents, drugs, chemical safety, endocrine disruptors, and emergent response for chemical hazard. These engines have been on our Web site for testing.

A Database for Propagation Models and Conversion to C++ Programming Language

NASA Technical Reports Server (NTRS)

Kantak, Anil V.; Angkasa, Krisjani; Rucker, James

1996-01-01

The telecommunications system design engineer generally needs the quantification of effects of the propagation medium (definition of the propagation channel) to design an optimal communications system. To obtain the definition of the channel, the systems engineer generally has a few choices. A search of the relevant publications such as the IEEE Transactions, CCIR's, NASA propagation handbook, etc., may be conducted to find the desired channel values. This method may need excessive amounts of time and effort on the systems engineer's part and there is a possibility that the search may not even yield the needed results. To help the researcher and the systems engineers, it was recommended by the conference participants of NASA Propagation Experimenters (NAPEX) XV (London, Ontario, Canada, June 28 and 29, 1991) that a software should be produced that would contain propagation models and the necessary prediction methods of most propagation phenomena. Moreover, the software should be flexible enough for the user to make slight changes to the models without expending a substantial effort in programming. In the past few years, a software was produced to fit these requirements as best as could be done. The software was distributed to all NAPEX participants for evaluation and use, the participant reactions, suggestions etc., were gathered and were used to improve the subsequent releases of the software. The existing database program is in the Microsoft Excel application software and works fine within the guidelines of that environment, however, recently there have been some questions about the robustness and survivability of the Excel software in the ever changing (hopefully improving) world of software packages.

The eSMAF: a software for the assessment and follow-up of functional autonomy in geriatrics

PubMed Central

Boissy, Patrick; Brière, Simon; Tousignant, Michel; Rousseau, Eric

2007-01-01

Background Functional status or disability forms the core of most assessment instruments used to identify mix and level of resources and services needed by older adults who possess common characteristics. The Functional Autonomy Measurement System (SMAF) is a 29-item scale measuring functional ability in five different areas. It has been recommended for use for home care, for allocation of chronic beds, for developing care plans in institutional settings and for epidemiological and evaluative studies. The SMAF can also be used with a case-mix classification system (Iso-SMAF) to allocate resources based on patients' functional autonomy characteristics. The objective of this project was to develop a software version of the SMAF to facilitate the evaluation of the functional status of older adults in health services research and to optimize the clinical decision-making process. Results The eSMAF was developed over an 24-month period using a modified waterfall software engineering process. Requirements and functional specifications were determined using focus groups of stakeholders. Different versions of the software were iteratively field-tested in clinical and research environments and software adaptations made accordingly. User documentation and online help were created to assist the deployment of the software. The software is available in French or English versions under a 30-day unregistered demonstration license or a free restricted registered academic license. It can be used locally on a Windows-based PC or over a network to input SMAF data into a database, search and aggregate client data according to clinical and/or administrative criteria, and generate summary or detailed reports of selected data sets for print or export to another database. Conclusion In the last year, the software has been successfully deployed in the clinical workflow of different institutions in research and clinical applications. The software performed relatively well in terms of stability and performance. Barriers to implementation included antiquated computer hardware, low computer literacy and access to IT support. Key factors for the deployment of the software included standardization of the workflow, user training and support. PMID:17298673

Problem Solving Software: What Does It Teach?

ERIC Educational Resources Information Center

Duffield, Judith A.

The purpose of this study was to examine the potential of computer-assisted instruction (CAI) for teaching problem solving skills. It was conducted in three phases. During the first phase, two pieces of problem solving software, "The King's Rule" and "Safari Search," were identified and analyzed. During the second phase, two groups of six…

A Look at Dialog's First CD-ROM Product.

ERIC Educational Resources Information Center

Duggan, Mary Kay

1987-01-01

Discusses reasons for selecting ERIC with the Dialog OnDisc software for training information professionals in online searching at the University of California, Berkeley, and analyzes some of the features of the CD-ROM software. Pros and cons of online and OnDisc access are summarized, and three references are listed. (Author/MES)

Hardwood log defect photographic database, software and user's guide

Treesearch

R. Edward Thomas

2009-01-01

Computer software and user's guide for Hardwood Log Defect Photographic Database. The database contains photographs and information on external hardwood log defects and the corresponding internal characteristics. This database allows users to search for specific defect types, sizes, and locations by tree species. For every defect, the database contains photos of...

Enterprise Resource Planning Software in the Human Resource Classroom

ERIC Educational Resources Information Center

Bedell, Michael D.; Floyd, Barry D.; Nicols, Kay McGlashan; Ellis, Rebecca

2007-01-01

The relatively recent development of comprehensive human resource information systems (HRIS) software has led to a large demand for technologically literate human resource (HR) professionals. For the college student who is about to begin the search for that first postcollege job, the need to develop technology literacy is even more necessary. To…

Kalman Filters for UXO Detection: Real-Time Feedback and Small Target Detection

DTIC Science & Technology

2012-05-01

last two decades. Accomplishments reported from both hardware and software point of views have moved the re- search focus from simple laboratory tests...quality data which in turn require a good positioning of the sensors atop the UXOs. The data collection protocol is currently based on a two-stage process...Note that this results is merely an illustration of the convergence of the Kalman filter. In practise , the linear part can be directly inverted for if

Finding collaborators: toward interactive discovery tools for research network systems.

PubMed

Borromeo, Charles D; Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-11-04

Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows.

Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems

PubMed Central

Schleyer, Titus K; Becich, Michael J; Hochheiser, Harry

2014-01-01

Background Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs. Objective The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype. Methods Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS). Results Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified. Conclusions Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows. PMID:25370463

Modification Site Localization in Peptides.

PubMed

Chalkley, Robert J

2016-01-01

There are a large number of search engines designed to take mass spectrometry fragmentation spectra and match them to peptides from proteins in a database. These peptides could be unmodified, but they could also bear modifications that were added biologically or during sample preparation. As a measure of reliability for the peptide identification, software normally calculates how likely a given quality of match could have been achieved at random, most commonly through the use of target-decoy database searching (Elias and Gygi, Nat Methods 4(3): 207-214, 2007). Matching the correct peptide but with the wrong modification localization is not a random match, so results with this error will normally still be assessed as reliable identifications by the search engine. Hence, an extra step is required to determine site localization reliability, and the software approaches to measure this are the subject of this part of the chapter.

A browsing tool for the Internet Logical Library of the HPCC Software Exchange

NASA Technical Reports Server (NTRS)

Biro, Ross

1993-01-01

As the quantity of information available on the Internet grows, locating a particular piece of information becomes more difficult. One possible solution is for a database of pointers to all available information to be maintained at a central site. Subject classifications for all the information could also be maintained in order to make searching possible. This paper describes one possible method of searching such an index. In particular a prototype browsing tool has been created using TCL/TK to demonstrate several possible features: rapidly scanning at any rank of the index, narrowing the index to any scope, regular-expression searching, and creation of a list of pointers answering to any set of index terms. The prototype browser is an easy-to-use independent X application designed for use in the Catalog of Repositories of the HPCC (High Performance Computing and Communications) Software Exchange.

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

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

Tolić, Nikola; Liu, Yina; Liyu, Andrey

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenatedmore » organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.« less

Realtime, Object-oriented Reduction of Parkes Multibeam Data using AIPS++

NASA Astrophysics Data System (ADS)

Barnes, D. G.

An overview of the Australia Telescope National Facility (ATNF) Parkes Multibeam Software is presented. The new thirteen-beam Parkes {21 cm} Multibeam Receiver is being used for the neutral hydrogen (Hi) Parkes All Sky Survey (HIPASS). This survey will search the entire southern sky for Hi in the redshift range {$-1200$ km s$^{-1}$} to {$+12600$ km s$^{-1}$}; with a limiting column density of {$N_Hi \\simeq 5 \\times 1017$ cm$^{-2}$}. Observations for the survey began in late February, 1997, and will continue through to the year 2000. A complete reduction package for the HIPASS survey has been developed, based on the AIPS++ library. The major software component is realtime, and uses advanced inter-process communication coupled to a graphical user interface, provided by AIPS++, to apply bandpass removal, flux calibration, velocity frame conversion and spectral smoothing to 26 spectra of 1024 channels each, every five seconds. AIPS++ connections have been added to ATNF-developed visualization software to provide on-line visual monitoring of the data quality. The non-realtime component of the software is responsible for gridding the spectra into position-velocity cubes; typically 200000 spectra are gridded into an $8^\\circ \\times 8^\\circ$ cube.

An improved hierarchical A * algorithm in the optimization of parking lots

NASA Astrophysics Data System (ADS)

Wang, Yong; Wu, Junjuan; Wang, Ying

2017-08-01

In the parking lot parking path optimization, the traditional evaluation index is the shortest distance as the best index and it does not consider the actual road conditions. Now, the introduction of a more practical evaluation index can not only simplify the hardware design of the boot system but also save the software overhead. Firstly, we establish the parking lot network graph RPCDV mathematical model and all nodes in the network is divided into two layers which were constructed using different evaluation function base on the improved hierarchical A * algorithm which improves the time optimal path search efficiency and search precision of the evaluation index. The final results show that for different sections of the program attribute parameter algorithm always faster the time to find the optimal path.

Formal methods for test case generation

NASA Technical Reports Server (NTRS)

Rushby, John (Inventor); De Moura, Leonardo Mendonga (Inventor); Hamon, Gregoire (Inventor)

2011-01-01

The invention relates to the use of model checkers to generate efficient test sets for hardware and software systems. The method provides for extending existing tests to reach new coverage targets; searching *to* some or all of the uncovered targets in parallel; searching in parallel *from* some or all of the states reached in previous tests; and slicing the model relative to the current set of coverage targets. The invention provides efficient test case generation and test set formation. Deep regions of the state space can be reached within allotted time and memory. The approach has been applied to use of the model checkers of SRI's SAL system and to model-based designs developed in Stateflow. Stateflow models achieving complete state and transition coverage in a single test case are reported.

Analysis of a mammography teaching program based on an affordance design model.

PubMed

Luo, Ping; Eikman, Edward A; Kealy, William; Qian, Wei

2006-12-01

The wide use of computer technology in education, particularly in mammogram reading, asks for e-learning evaluation. The existing media comparative studies, learner attitude evaluations, and performance tests are problematic. Based on an affordance design model, this study examined an existing e-learning program on mammogram reading. The selection criteria include content relatedness, representativeness, e-learning orientation, image quality, program completeness, and accessibility. A case study was conducted to examine the affordance features, functions, and presentations of the selected software. Data collection and analysis methods include interviews, protocol-based document analysis, and usability tests and inspection. Also some statistics were calculated. The examination of PBE identified that this educational software designed and programmed some tools. The learner can use these tools in the process of optimizing displays, scanning images, comparing different projections, marking the region of interests, constructing a descriptive report, assessing one's learning outcomes, and comparing one's decisions with the experts' decisions. Further, PBE provides some resources for the learner to construct one's knowledge and skills, including a categorized image library, a term-searching function, and some teaching links. Besides, users found it easy to navigate and carry out tasks. The users also reacted positively toward PBE's navigation system, instructional aids, layout, pace and flow of information, graphics, and other presentation design. The software provides learners with some cognitive tools, supporting their perceptual problem-solving processes and extending their capabilities. Learners can internalize the mental models in mammogram reading through multiple perceptual triangulations, sensitization of related features, semantic description of mammogram findings, and expert-guided semantic report construction. The design of these cognitive tools and the software interface matches the findings and principles in human learning and instructional design. Working with PBE's case-based simulations and categorized gallery, learners can enrich and transfer their experience to their jobs.

NASA Tech Briefs, January 2003

NASA Technical Reports Server (NTRS)

2003-01-01

Topics covered include: Optoelectronic Tool Adds Scale Marks to Photographic Images; Compact Interconnection Networks Based on Quantum Dots; Laterally Coupled Quantum-Dot Distributed-Feedback Lasers; Bit-Serial Adder Based on Quantum Dots; Stabilized Fiber-Optic Distribution of Reference Frequency; Delay/Doppler-Mapping GPS-Reflection Remote-Sensing System; Ladar System Identifies Obstacles Partly Hidden by Grass; Survivable Failure Data Recorders for Spacecraft; Fiber-Optic Ammonia Sensors; Silicon Membrane Mirrors with Electrostatic Shape Actuators; Nanoscale Hot-Wire Probes for Boundary-Layer Flows; Theodolite with CCD Camera for Safe Measurement of Laser-Beam Pointing; Efficient Coupling of Lasers to Telescopes with Obscuration; Aligning Three Off-Axis Mirrors with Help of a DOE; Calibrating Laser Gas Measurements by Use of Natural CO2; Laser Ranging Simulation Program; Micro-Ball-Lens Optical Switch Driven by SMA Actuator; Evaluation of Charge Storage and Decay in Spacecraft Insulators; Alkaline Capacitors Based on Nitride Nanoparticles; Low-EC-Content Electrolytes for Low-Temperature Li-Ion Cells; Software for a GPS-Reflection Remote-Sensing System; Software for Building Models of 3D Objects via the Internet; "Virtual Cockpit Window" for a Windowless Aerospacecraft; CLARAty Functional-Layer Software; Java Library for Input and Output of Image Data and Metadata; Software for Estimating Costs of Testing Rocket Engines; Energy-Absorbing, Lightweight Wheels; Viscoelastic Vibration Dampers for Turbomachine Blades; Soft Landing of Spacecraft on Energy-Absorbing Self-Deployable Cushions; Pneumatically Actuated Miniature Peristaltic Vacuum Pumps; Miniature Gas-Turbine Power Generator; Pressure-Sensor Assembly Technique; Wafer-Level Membrane-Transfer Process for Fabricating MEMS; A Reactive-Ion Etch for Patterning Piezoelectric Thin Film; Wavelet-Based Real-Time Diagnosis of Complex Systems; Quantum Search in Hilbert Space; Analytic Method for Computing Instrument Pointing Jitter; and Semiselective Optoelectronic Sensors for Monitoring Microbes.

PCI bus content-addressable-memory (CAM) implementation on FPGA for pattern recognition/image retrieval in a distributed environment

NASA Astrophysics Data System (ADS)

Megherbi, Dalila B.; Yan, Yin; Tanmay, Parikh; Khoury, Jed; Woods, C. L.

2004-11-01

Recently surveillance and Automatic Target Recognition (ATR) applications are increasing as the cost of computing power needed to process the massive amount of information continues to fall. This computing power has been made possible partly by the latest advances in FPGAs and SOPCs. In particular, to design and implement state-of-the-Art electro-optical imaging systems to provide advanced surveillance capabilities, there is a need to integrate several technologies (e.g. telescope, precise optics, cameras, image/compute vision algorithms, which can be geographically distributed or sharing distributed resources) into a programmable system and DSP systems. Additionally, pattern recognition techniques and fast information retrieval, are often important components of intelligent systems. The aim of this work is using embedded FPGA as a fast, configurable and synthesizable search engine in fast image pattern recognition/retrieval in a distributed hardware/software co-design environment. In particular, we propose and show a low cost Content Addressable Memory (CAM)-based distributed embedded FPGA hardware architecture solution with real time recognition capabilities and computing for pattern look-up, pattern recognition, and image retrieval. We show how the distributed CAM-based architecture offers a performance advantage of an order-of-magnitude over RAM-based architecture (Random Access Memory) search for implementing high speed pattern recognition for image retrieval. The methods of designing, implementing, and analyzing the proposed CAM based embedded architecture are described here. Other SOPC solutions/design issues are covered. Finally, experimental results, hardware verification, and performance evaluations using both the Xilinx Virtex-II and the Altera Apex20k are provided to show the potential and power of the proposed method for low cost reconfigurable fast image pattern recognition/retrieval at the hardware/software co-design level.

Specification for a surface-search radar-detection-range model

NASA Astrophysics Data System (ADS)

Hattan, Claude P.

1990-09-01

A model that predicts surface-search radar detection range versus a variety of combatants has been developed at the Naval Ocean Systems Center. This model uses a simplified ship radar cross section (RCS) model and the U.S. Navy Oceanographic and Atmospheric Mission Library Standard Electromagnetic Propagation Model. It provides the user with a method of assessing the effects of the environment of the performance of a surface-search radar system. The software implementation of the model is written in ANSI FORTRAN 77, with MIL-STD-1753 extensions. The program provides the user with a table of expected detection ranges when the model is supplied with the proper environmental radar system inputs. The target model includes the variation in RCS as a function of aspect angle and the distribution of reflected radar energy as a function of height above the waterline. The modeled propagation effects include refraction caused by a multisegmented refractivity profile, sea-surface roughness caused by local winds, evaporation ducting, and surface-based ducts caused by atmospheric layering.

The future of bibliographic standards in a networked information environment

NASA Technical Reports Server (NTRS)

1997-01-01

The main mission of the CENDI Cataloging Working Group is to provide guidelines for cataloging practices that support the sharing of database records among the CENDI agencies, and that incorporate principles based on cost effectiveness and efficiency. Recent efforts include the extension of COSATI Guidelines for the Cataloging of Technical Reports to include non-print materials, and the mapping of each agency's export file structure to USMARC. Of primary importance is the impact of electronic documents and the distributed nature of the networked information environment. Topics discussed during the workshop include the following: Trade-offs in Cataloging and Indexing Internet Information; The Impact on Current and Future Standards; A Look at WWW Metadata Initiatives; Standards for Electronic Journals; The Present and Future Search Engines; The Roles for Text Analysis Software; Advanced Search Engine Meets Metathesaurus; Locator Schemes for Internet Resources; Identifying and Cataloging Web Document Types; In Search of a New Bibliographic Record. The videos in this set include viewgraphs of charts and related materials of the workshop.

QuickVina: accelerating AutoDock Vina using gradient-based heuristics for global optimization.

PubMed

Handoko, Stephanus Daniel; Ouyang, Xuchang; Su, Chinh Tran To; Kwoh, Chee Keong; Ong, Yew Soon

2012-01-01

Predicting binding between macromolecule and small molecule is a crucial phase in the field of rational drug design. AutoDock Vina, one of the most widely used docking software released in 2009, uses an empirical scoring function to evaluate the binding affinity between the molecules and employs the iterated local search global optimizer for global optimization, achieving a significantly improved speed and better accuracy of the binding mode prediction compared its predecessor, AutoDock 4. In this paper, we propose further improvement in the local search algorithm of Vina by heuristically preventing some intermediate points from undergoing local search. Our improved version of Vina-dubbed QVina-achieved a maximum acceleration of about 25 times with the average speed-up of 8.34 times compared to the original Vina when tested on a set of 231 protein-ligand complexes while maintaining the optimal scores mostly identical. Using our heuristics, larger number of different ligands can be quickly screened against a given receptor within the same time frame.

The Biomolecular Crystallization Database Version 4: expanded content and new features.

PubMed

Tung, Michael; Gallagher, D Travis

2009-01-01

The Biological Macromolecular Crystallization Database (BMCD) has been a publicly available resource since 1988, providing a curated archive of information on crystal growth for proteins and other biological macromolecules. The BMCD content has recently been expanded to include 14 372 crystal entries. The resource continues to be freely available at http://xpdb.nist.gov:8060/BMCD4. In addition, the software has been adapted to support the Java-based Lucene query language, enabling detailed searching over specific parameters, and explicit search of parameter ranges is offered for five numeric variables. Extensive tools have been developed for import and handling of data from the RCSB Protein Data Bank. The updated BMCD is called version 4.02 or BMCD4. BMCD4 entries have been expanded to include macromolecule sequence, enabling more elaborate analysis of relations among protein properties, crystal-growth conditions and the geometric and diffraction properties of the crystals. The BMCD version 4.02 contains greatly expanded content and enhanced search capabilities to facilitate scientific analysis and design of crystal-growth strategies.

Interventions to Improve the Quality of Outpatient Specialty Referral Requests: A Systematic Review.

PubMed

Hendrickson, Chase D; Lacourciere, Stacy L; Zanetti, Cole A; Donaldson, Patrick C; Larson, Robin J

2016-09-01

Requests for outpatient specialty consultations occur frequently but often are of poor quality because of incompleteness. The authors searched bibliographic databases, trial registries, and references during October 2014 for studies evaluating interventions to improve the quality of outpatient specialty referral requests compared to usual practice. Two reviewers independently extracted data and assessed quality. Findings were qualitatively summarized for completeness of information relayed in a referral request within naturally emerging intervention categories. Of 3495 articles screened, 11 were eligible. All 3 studies evaluating software-based interventions found statistically significant improvements. Among 4 studies evaluating template/pro forma interventions, completeness was uniformly improved but with variable or unreported statistical significance. Of 4 studies evaluating educational interventions, 2 favored the intervention and 2 found no difference. One study evaluating referral management was negative. Current evidence for improving referral request quality is strongest for software-based interventions and templates, although methodological quality varied and findings may be setting specific. © The Author(s) 2015.

Knowledge assistant for robotic environmental characterization

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

Feddema, J.; Rivera, J.; Tucker, S.

1996-08-01

A prototype sensor fusion framework called the {open_quotes}Knowledge Assistant{close_quotes} has been developed and tested on a gantry robot at Sandia National Laboratories. This Knowledge Assistant guides the robot operator during the planning, execution, and post analysis stages of the characterization process. During the planning stage, the Knowledge Assistant suggests robot paths and speeds based on knowledge of sensors available and their physical characteristics. During execution, the Knowledge Assistant coordinates the collection of data through a data acquisition {open_quotes}specialist.{close_quotes} During execution and postanalysis, the Knowledge Assistant sends raw data to other {open_quotes}specialists,{close_quotes} which include statistical pattern recognition software, a neural network,more » and model-based search software. After the specialists return their results, the Knowledge Assistant consolidates the information and returns a report to the robot control system where the sensed objects and their attributes (e.g., estimated dimensions, weight, material composition, etc.) are displayed in the world model. This report highlights the major components of this system.« less

High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting

PubMed Central

Bogdán, István A.; Rivers, Jenny; Beynon, Robert J.; Coca, Daniel

2008-01-01

Motivation: Peptide mass fingerprinting (PMF) is a method for protein identification in which a protein is fragmented by a defined cleavage protocol (usually proteolysis with trypsin), and the masses of these products constitute a ‘fingerprint’ that can be searched against theoretical fingerprints of all known proteins. In the first stage of PMF, the raw mass spectrometric data are processed to generate a peptide mass list. In the second stage this protein fingerprint is used to search a database of known proteins for the best protein match. Although current software solutions can typically deliver a match in a relatively short time, a system that can find a match in real time could change the way in which PMF is deployed and presented. In a paper published earlier we presented a hardware design of a raw mass spectra processor that, when implemented in Field Programmable Gate Array (FPGA) hardware, achieves almost 170-fold speed gain relative to a conventional software implementation running on a dual processor server. In this article we present a complementary hardware realization of a parallel database search engine that, when running on a Xilinx Virtex 2 FPGA at 100 MHz, delivers 1800-fold speed-up compared with an equivalent C software routine, running on a 3.06 GHz Xeon workstation. The inherent scalability of the design means that processing speed can be multiplied by deploying the design on multiple FPGAs. The database search processor and the mass spectra processor, running on a reconfigurable computing platform, provide a complete real-time PMF protein identification solution. Contact: d.coca@sheffield.ac.uk PMID:18453553

The Philip Morris Information Network: A Library Database on an In-House Timesharing System.

ERIC Educational Resources Information Center

DeBardeleben, Marian Z.; And Others

1983-01-01

Outlines a database constructed at Philip Morris Research Center Library which encompasses holdings and circulation and acquisitions records for all items in the library. Host computer (DECSYSTEM-2060), software (BASIC), database design, search methodology, cataloging, and accessibility are noted; sample search, circ-in profile, end user profiles,…

Graphing Online Searches with Lotus 1-2-3.

ERIC Educational Resources Information Center

Persson, Olle

1986-01-01

This article illustrates how Lotus 1-2-3 software can be used to create graphs using downloaded online searches as raw material, notes most commands applied, and outlines three required steps: downloading, importing the downloading file into the worksheet, and making graphs. An example in bibliometrics and sample graphs are included. (EJS)

Tools to Ease Your Internet Adventures: Part I.

ERIC Educational Resources Information Center

Descy, Don E.

1993-01-01

This first of a two-part series highlights three tools that improve accessibility to Internet resources: (1) Alex, a database that accesses files in FTP (file transfer protocol) sites; (2) Archie, software that searches for file names with a user's search term; and (3) Gopher, a menu-driven program to access Internet sites. (LRW)

Kodak Picture Exchange--Online Access to Photographs and Images.

ERIC Educational Resources Information Center

Valauskas, Edward J.

1995-01-01

Describes the Kodak Picture Exchange that includes a database of over 200,000 photographic images collected from 28 stock photography companies in the United States that allows the user to search for images by topic. Highlights include installing the software, alternative search strategies, costs, manipulating images, and rules governing the use…

Objectives and first results of the NASA SETI sky survey field tests at Goldstone

NASA Technical Reports Server (NTRS)

Gulkis, S.; Klein, M. J.; Olsen, E. T.; Crow, R. B.; Gosline, R. M.; Downs, G. S.; Quirk, M. P.; Lokshin, A.; Solomon, J.

1986-01-01

Field tests of SETI (Search for Extraterrestrial Intelligence) prototype hardware and software began in March 1985 at Goldstone. With emphasis on the sky survey component of the NASA SETI search strategy, the article describes the survey characteristics, the detection strategy, and preliminary results of system tests.

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

Software Applications to Access Earth Science Data: Building an ECHO Client

NASA Astrophysics Data System (ADS)

Cohen, A.; Cechini, M.; Pilone, D.

2010-12-01

Historically, developing an ECHO (NASA’s Earth Observing System (EOS) ClearingHOuse) client required interaction with its SOAP API. SOAP, as a framework for web service communication has numerous advantages for Enterprise applications and Java/C# type programming languages. However, as interest has grown for quick development cycles and more intriguing “mashups,” ECHO has seen the SOAP API lose its appeal. In order to address these changing needs, ECHO has introduced two new interfaces facilitating simple access to its metadata holdings. The first interface is built upon the OpenSearch format and ESIP Federated Search framework. The second interface is built upon the Representational State Transfer (REST) architecture. Using the REST and OpenSearch APIs to access ECHO makes development with modern languages much more feasible and simpler. Client developers can leverage the simple interaction with ECHO to focus more of their time on the advanced functionality they are presenting to users. To demonstrate the simplicity of developing with the REST API, participants will be led through a hands-on experience where they will develop an ECHO client that performs the following actions: + Login + Provider discovery + Provider based dataset discovery + Dataset, Temporal, and Spatial constraint based Granule discovery + Online Data Access

Local motion compensation in image sequences degraded by atmospheric turbulence: a comparative analysis of optical flow vs. block matching methods

NASA Astrophysics Data System (ADS)

Huebner, Claudia S.

2016-10-01

As a consequence of fluctuations in the index of refraction of the air, atmospheric turbulence causes scintillation, spatial and temporal blurring as well as global and local image motion creating geometric distortions. To mitigate these effects many different methods have been proposed. Global as well as local motion compensation in some form or other constitutes an integral part of many software-based approaches. For the estimation of motion vectors between consecutive frames simple methods like block matching are preferable to more complex algorithms like optical flow, at least when challenged with near real-time requirements. However, the processing power of commercially available computers continues to increase rapidly and the more powerful optical flow methods have the potential to outperform standard block matching methods. Therefore, in this paper three standard optical flow algorithms, namely Horn-Schunck (HS), Lucas-Kanade (LK) and Farnebäck (FB), are tested for their suitability to be employed for local motion compensation as part of a turbulence mitigation system. Their qualitative performance is evaluated and compared with that of three standard block matching methods, namely Exhaustive Search (ES), Adaptive Rood Pattern Search (ARPS) and Correlation based Search (CS).

Real-time access of large volume imagery through low-bandwidth links

NASA Astrophysics Data System (ADS)

Phillips, James; Grohs, Karl; Brower, Bernard; Kelly, Lawrence; Carlisle, Lewis; Pellechia, Matthew

2010-04-01

Providing current, time-sensitive imagery and geospatial information to deployed tactical military forces or first responders continues to be a challenge. This challenge is compounded through rapid increases in sensor collection volumes, both with larger arrays and higher temporal capture rates. Focusing on the needs of these military forces and first responders, ITT developed a system called AGILE (Advanced Geospatial Imagery Library Enterprise) Access as an innovative approach based on standard off-the-shelf techniques to solving this problem. The AGILE Access system is based on commercial software called Image Access Solutions (IAS) and incorporates standard JPEG 2000 processing. Our solution system is implemented in an accredited, deployable form, incorporating a suite of components, including an image database, a web-based search and discovery tool, and several software tools that act in concert to process, store, and disseminate imagery from airborne systems and commercial satellites. Currently, this solution is operational within the U.S. Government tactical infrastructure and supports disadvantaged imagery users in the field. This paper presents the features and benefits of this system to disadvantaged users as demonstrated in real-world operational environments.

Databank Software for the 1990s and Beyond--Part 1: The User's Wish List.

ERIC Educational Resources Information Center

Basch, Reva

1990-01-01

Describes desired software enhancements identified by the Southern California Online Users Group in the areas of search language, database selection, document retrieval and display, user interface, customer support, and cost and economic issues. The need to prioritize these wishes and to determine whether features should reside in the mainframe or…

Photo-Pictures and Dynamic Software or about the Motivation of the Art-Oriented Students

ERIC Educational Resources Information Center

Chehlarova, Toni; Chehlarova, Koya

2014-01-01

This paper deals with ideas about dynamic presentation of photo-pictures by means of dynamic software GeoGebra in order to motivate art students to get acquainted with some specific mathematical functions. The results of the experiment include deeper understanding of the functions' nature, search of new functions for dealing with a practical…

Automating Reference Desk Files with Microcomputers in a Public Library: An Exploration of Data Resources, Methods, and Software.

ERIC Educational Resources Information Center

Miley, David W.

Many reference librarians still rely on manual searches to access vertical files, ready reference files, and other information stored in card files, drawers, and notebooks scattered around the reference department. Automated access to these materials via microcomputers using database management software may speed up the process. This study focuses…

HSI-Find: A Visualization and Search Service for Terascale Spectral Image Catalogs

NASA Astrophysics Data System (ADS)

Thompson, D. R.; Smith, A. T.; Castano, R.; Palmer, E. E.; Xing, Z.

2013-12-01

Imaging spectrometers are remote sensing instruments commonly deployed on aircraft and spacecraft. They provide surface reflectance in hundreds of wavelength channels, creating data cubes known as hyperspecrtral images. They provide rich compositional information making them powerful tools for planetary and terrestrial science. These data products can be challenging to interpret because they contain datapoints numbering in the thousands (Dawn VIR) or millions (AVIRIS-C). Cross-image studies or exploratory searches involving more than one scene are rare; data volumes are often tens of GB per image and typical consumer-grade computers cannot store more than a handful of images in RAM. Visualizing the information in a single scene is challenging since the human eye can only distinguish three color channels out of the hundreds available. To date, analysis has been performed mostly on single images using purpose-built software tools that require extensive training and commercial licenses. The HSIFind software suite provides a scalable distributed solution to the problem of visualizing and searching large catalogs of spectral image data. It consists of a RESTful web service that communicates to a javascript-based browser client. The software provides basic visualization through an intuitive visual interface, allowing users with minimal training to explore the images or view selected spectra. Users can accumulate a library of spectra from one or more images and use these to search for similar materials. The result appears as an intensity map showing the extent of a spectral feature in a scene. Continuum removal can isolate diagnostic absorption features. The server-side mapping algorithm uses an efficient matched filter algorithm that can process a megapixel image cube in just a few seconds. This enables real-time interaction, leading to a new way of interacting with the data: the user can launch a search with a single mouse click and see the resulting map in seconds. This allows the user to quickly explore each image, ascertain the main units of surface material, localize outliers, and develop an understanding of the various materials' spectral characteristics. The HSIFind software suite is currently in beta testing at the Planetary Science Institute and a process is underway to release it under an open source license to the broader community. We believe it will benefit instrument operations during remote planetary exploration, where tactical mission decisions demand rapid analysis of each new dataset. The approach also holds potential for public spectral catalogs where its shallow learning curve and portability can make these datasets accessible to a much wider range of researchers. Acknowledgements: The HSIFind project acknowledges the NASA Advanced MultiMission Operating System (AMMOS) and the Multimission Ground Support Services (MGSS). E. Palmer is with the Planetary Science Institute, Tucson, AZ. Other authors are with the Jet Propulsion Laboratory, Pasadena, CA. This work was carried out at the Jet Propulsion Laboratory, California Institute of Technology under a contract with the National Aeronautics and Space Administration. Copyright 2013, California Institute of Technology.

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

Egnos-Based Multi-Sensor Accurate and Reliable Navigation in Search-And Missions with Uavs

NASA Astrophysics Data System (ADS)

Molina, P.; Colomina, I.; Vitoria, T.; Silva, P. F.; Stebler, Y.; Skaloud, J.; Kornus, W.; Prades, R.

2011-09-01

This paper will introduce and describe the goals, concept and overall approach of the European 7th Framework Programme's project named CLOSE-SEARCH, which stands for 'Accurate and safe EGNOS-SoL Navigation for UAV-based low-cost SAR operations'. The goal of CLOSE-SEARCH is to integrate in a helicopter-type unmanned aerial vehicle, a thermal imaging sensor and a multi-sensor navigation system (based on the use of a Barometric Altimeter (BA), a Magnetometer (MAGN), a Redundant Inertial Navigation System (RINS) and an EGNOS-enabled GNSS receiver) with an Autonomous Integrity Monitoring (AIM) capability, to support the search component of Search-And-Rescue operations in remote, difficult-to-access areas and/or in time critical situations. The proposed integration will result in a hardware and software prototype that will demonstrate an end-to-end functionality, that is to fly in patterns over a region of interest (possibly inaccessible) during day or night and also under adverse weather conditions and locate there disaster survivors or lost people through the detection of the body heat. This paper will identify the technical challenges of the proposed approach, from navigating with a BA/MAGN/RINS/GNSS-EGNOSbased integrated system to the interpretation of thermal images for person identification. Moreover, the AIM approach will be described together with the proposed integrity requirements. Finally, this paper will show some results obtained in the project during the first test campaign performed on November 2010. On that day, a prototype was flown in three different missions to assess its high-level performance and to observe some fundamental mission parameters as the optimal flying height and flying speed to enable body recognition. The second test campaign is scheduled for the end of 2011.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

Harnessing Scientific Literature Reports for Pharmacovigilance

PubMed Central

Ripple, Anna; Tonning, Joseph; Munoz, Monica; Hasan, Rashedul; Ly, Thomas; Francis, Henry; Bodenreider, Olivier

2017-01-01

Summary Objectives We seek to develop a prototype software analytical tool to augment FDA regulatory reviewers’ capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool. Methods A prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use. Results All usability test participants cited the tool’s ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool’s automated literature search relative to a manual ‘all fields’ PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools. Conclusions Usability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction. PMID:28326432

A microcontroller-based three degree-of-freedom manipulator testbed. M.S. Thesis

NASA Technical Reports Server (NTRS)

Brown, Robert Michael, Jr.

1995-01-01

A wheeled exploratory vehicle is under construction at the Mars Mission Research Center at North Carolina State University. In order to serve as more than an inspection tool, this vehicle requires the ability to interact with its surroundings. A crane-type manipulator, as well as the necessary control hardware and software, has been developed for use as a sample gathering tool on this vehicle. The system is controlled by a network of four Motorola M68HC11 microcontrollers. Control hardware and software were developed in a modular fashion so that the system can be used to test future control algorithms and hardware. Actuators include three stepper motors and one solenoid. Sensors include three optical encoders and one cable tensiometer. The vehicle supervisor computer provides the manipulator system with the approximate coordinates of the target object. This system maps the workspace surrounding the given location by lowering the claw, along a set of evenly spaced vertical lines, until contact occurs. Based on this measured height information and prior knowledge of the target object size, the system determines if the object exists in the searched area. The system can find and retrieve a 1.25 in. diameter by 1.25 in. tall cylinder placed within the 47.5 sq in search area in less than 12 minutes. This manipulator hardware may be used for future control algorithm verification and serves as a prototype for other manipulator hardware.

BEESCOUT: A model of bee scouting behaviour and a software tool for characterizing nectar/pollen landscapes for BEEHAVE.

PubMed

Becher, M A; Grimm, V; Knapp, J; Horn, J; Twiston-Davies, G; Osborne, J L

2016-11-24

Social bees are central place foragers collecting floral resources from the surrounding landscape, but little is known about the probability of a scouting bee finding a particular flower patch. We therefore developed a software tool, BEESCOUT, to theoretically examine how bees might explore a landscape and distribute their scouting activities over time and space. An image file can be imported, which is interpreted by the model as a "forage map" with certain colours representing certain crops or habitat types as specified by the user. BEESCOUT calculates the size and location of these potential food sources in that landscape relative to a bee colony. An individual-based model then determines the detection probabilities of the food patches by bees, based on parameter values gathered from the flight patterns of radar-tracked honeybees and bumblebees. Various "search modes" describe hypothetical search strategies for the long-range exploration of scouting bees. The resulting detection probabilities of forage patches can be used as input for the recently developed honeybee model BEEHAVE, to explore realistic scenarios of colony growth and death in response to different stressors. In example simulations, we find that detection probabilities for food sources close to the colony fit empirical data reasonably well. However, for food sources further away no empirical data are available to validate model output. The simulated detection probabilities depend largely on the bees' search mode, and whether they exchange information about food source locations. Nevertheless, we show that landscape structure and connectivity of food sources can have a strong impact on the results. We believe that BEESCOUT is a valuable tool to better understand how landscape configurations and searching behaviour of bees affect detection probabilities of food sources. It can also guide the collection of relevant data and the design of experiments to close knowledge gaps, and provides a useful extension to the BEEHAVE honeybee model, enabling future users to explore how landscape structure and food availability affect the foraging decisions and patch visitation rates of the bees and, in consequence, to predict colony development and survival.

A comparative study of the A* heuristic search algorithm used to solve efficiently a puzzle game

NASA Astrophysics Data System (ADS)

Iordan, A. E.

2018-01-01

The puzzle game presented in this paper consists in polyhedra (prisms, pyramids or pyramidal frustums) which can be moved using the free available spaces. The problem requires to be found the minimum number of movements in order the game reaches to a goal configuration starting from an initial configuration. Because the problem is enough complex, the principal difficulty in solving it is given by dimension of search space, that leads to necessity of a heuristic search. The improving of the search method consists into determination of a strong estimation by the heuristic function which will guide the search process to the most promising side of the search tree. The comparative study is realized among Manhattan heuristic and the Hamming heuristic using A* search algorithm implemented in Java. This paper also presents the necessary stages in object oriented development of a software used to solve efficiently this puzzle game. The modelling of the software is achieved through specific UML diagrams representing the phases of analysis, design and implementation, the system thus being described in a clear and practical manner. With the purpose to confirm the theoretical results which demonstrates that Manhattan heuristic is more efficient was used space complexity criterion. The space complexity was measured by the number of generated nodes from the search tree, by the number of the expanded nodes and by the effective branching factor. From the experimental results obtained by using the Manhattan heuristic, improvements were observed regarding space complexity of A* algorithm versus Hamming heuristic.

BEAUTY-X: enhanced BLAST searches for DNA queries.

PubMed

Worley, K C; Culpepper, P; Wiese, B A; Smith, R F

1998-01-01

BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced version of the BLAST database search tool that facilitates identification of the functions of matched sequences. Three recent improvements to the BEAUTY program described here make the enhanced output (1) available for DNA queries, (2) available for searches of any protein database, and (3) more up-to-date, with periodic updates of the domain information. BEAUTY searches of the NCBI and EMBL non-redundant protein sequence databases are available from the BCM Search Launcher Web pages (http://gc.bcm.tmc. edu:8088/search-launcher/launcher.html). BEAUTY Post-Processing of submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html (kworley,culpep)@bcm.tmc.edu

Harmony Search as a Powerful Tool for Feature Selection in QSPR Study of the Drugs Lipophilicity.

PubMed

Bahadori, Behnoosh; Atabati, Morteza

2017-01-01

Aims & Scope: Lipophilicity represents one of the most studied and most frequently used fundamental physicochemical properties. In the present work, harmony search (HS) algorithm is suggested to feature selection in quantitative structure-property relationship (QSPR) modeling to predict lipophilicity of neutral, acidic, basic and amphotheric drugs that were determined by UHPLC. Harmony search is a music-based metaheuristic optimization algorithm. It was affected by the observation that the aim of music is to search for a perfect state of harmony. Semi-empirical quantum-chemical calculations at AM1 level were used to find the optimum 3D geometry of the studied molecules and variant descriptors (1497 descriptors) were calculated by the Dragon software. The selected descriptors by harmony search algorithm (9 descriptors) were applied for model development using multiple linear regression (MLR). In comparison with other feature selection methods such as genetic algorithm and simulated annealing, harmony search algorithm has better results. The root mean square error (RMSE) with and without leave-one out cross validation (LOOCV) were obtained 0.417 and 0.302, respectively. The results were compared with those obtained from the genetic algorithm and simulated annealing methods and it showed that the HS is a helpful tool for feature selection with fine performance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

An intelligent, free-flying robot

NASA Technical Reports Server (NTRS)

Reuter, G. J.; Hess, C. W.; Rhoades, D. E.; Mcfadin, L. W.; Healey, K. J.; Erickson, J. D.

1988-01-01

The ground-based demonstration of EVA Retriever, a voice-supervised, intelligent, free-flying robot, is designed to evaluate the capability to retrieve objects (astronauts, equipment, and tools) which have accidentally separated from the Space Station. The major objective of the EVA Retriever Project is to design, develop, and evaluate an integrated robotic hardware and on-board software system which autonomously: (1) performs system activation and check-out, (2) searches for and acquires the target, (3) plans and executes a rendezvous while continuously tracking the target, (4) avoids stationary and moving obstacles, (5) reaches for and grapples the target, (6) returns to transfer the object, and (7) returns to base.

An intelligent, free-flying robot

NASA Technical Reports Server (NTRS)

Reuter, G. J.; Hess, C. W.; Rhoades, D. E.; Mcfadin, L. W.; Healey, K. J.; Erickson, J. D.; Phinney, Dale E.

1989-01-01

The ground based demonstration of the extensive extravehicular activity (EVA) Retriever, a voice-supervised, intelligent, free flying robot, is designed to evaluate the capability to retrieve objects (astronauts, equipment, and tools) which have accidentally separated from the Space Station. The major objective of the EVA Retriever Project is to design, develop, and evaluate an integrated robotic hardware and on-board software system which autonomously: (1) performs system activation and check-out; (2) searches for and acquires the target; (3) plans and executes a rendezvous while continuously tracking the target; (4) avoids stationary and moving obstacles; (5) reaches for and grapples the target; (6) returns to transfer the object; and (7) returns to base.

NASA integrated vehicle health management technology experiment for X-37

NASA Astrophysics Data System (ADS)

Schwabacher, Mark; Samuels, Jeff; Brownston, Lee

2002-07-01

The NASA Integrated Vehicle Health Management (IVHM) Technology Experiment for X-37 was intended to run IVHM software on board the X-37 spacecraft. The X-37 is an unpiloted vehicle designed to orbit the Earth for up to 21 days before landing on a runway. The objectives of the experiment were to demonstrate the benefits of in-flight IVHM to the operation of a Reusable Launch Vehicle, to advance the Technology Readiness Level of this IVHM technology within a flight environment, and to demonstrate that the IVHM software could operate on the Vehicle Management Computer. The scope of the experiment was to perform real-time fault detection and isolation for X-37's electrical power system and electro-mechanical actuators. The experiment used Livingstone, a software system that performs diagnosis using a qualitative, model-based reasoning approach that searches system-wide interactions to detect and isolate failures. Two of the challenges we faced were to make this research software more efficient so that it would fit within the limited computational resources that were available to us on the X-37 spacecraft, and to modify it so that it satisfied the X-37's software safety requirements. Although the experiment is currently unfunded, the development effort resulted in major improvements in Livingstone's efficiency and safety. This paper reviews some of the details of the modeling and integration efforts, and some of the lessons that were learned.

Application of the Golden Software Surfer mapping software for automation of visualisation of meteorological and oceanographic data in IMGW Maritime Branch.

NASA Astrophysics Data System (ADS)

Piliczewski, B.

2003-04-01

The Golden Software Surfer has been used in IMGW Maritime Branch for more than ten years. This tool provides ActiveX Automation objects, which allow scripts to control practically every feature of Surfer. These objects can be accessed from any Automation-enabled environment, such as Visual Basic or Excel. Several applications based on Surfer has been developed in IMGW. The first example is an on-line oceanographic service, which presents forecasts of the water temperature, sea level and currents originating from the HIROMB model and is automatically updated every day. Surfer was also utilised in MERMAID, an international project supported by EC under the 5th Framework Programme. The main aim of this project was to create a prototype of the Internet-based data brokerage system, which would enable to search, extract, buy and download datasets containing meteorological or oceanographic data. During the project IMGW developed an online application, called Mermaid Viewer, which enables communication with the data broker and automatic visualisation of the downloaded data using Surfer. Both the above mentioned applications were developed in Visual Basic. Currently it is considered to adopt Surfer for the monitoring service, which provides access to the data collected in the monitoring of the Baltic Sea environment.

76 FR 21017 - United States v. Google Inc. and ITA Software Inc., Proposed Final Judgment and Competitive...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-14

.... Google seeks to expand its search services by launching an Internet travel site to offer comparative... and other companies offering travel-related products and services. 14. Metas enable consumers to search for flights but do not offer booking services. When a consumer on a Meta travel site enters a...

Open-Source Tools for Enhancing Full-Text Searching of OPACs: Use of Koha, Greenstone and Fedora

ERIC Educational Resources Information Center

Anuradha, K. T.; Sivakaminathan, R.; Kumar, P. Arun

2011-01-01

Purpose: There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text…

Cloud based, Open Source Software Application for Mitigating Herbicide Drift

NASA Astrophysics Data System (ADS)

Saraswat, D.; Scott, B.

2014-12-01

The spread of herbicide resistant weeds has resulted in the need for clearly marked fields. In response to this need, the University of Arkansas Cooperative Extension Service launched a program named Flag the Technology in 2011. This program uses color-coded flags as a visual alert of the herbicide trait technology within a farm field. The flag based program also serves to help avoid herbicide misapplication and prevent herbicide drift damage between fields with differing crop technologies. This program has been endorsed by Southern Weed Science Society of America and is attracting interest from across the USA, Canada, and Australia. However, flags have risk of misplacement or disappearance due to mischief or severe windstorms/thunderstorms, respectively. This presentation will discuss the design and development of a cloud-based, free application utilizing open-source technologies, called Flag the Technology Cloud (FTTCloud), for allowing agricultural stakeholders to color code their farm fields for indicating herbicide resistant technologies. The developed software utilizes modern web development practices, widely used design technologies, and basic geographic information system (GIS) based interactive interfaces for representing, color-coding, searching, and visualizing fields. This program has also been made compatible for a wider usability on different size devices- smartphones, tablets, desktops and laptops.

GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns

DOE PAGES

Senin, Pavel; Lin, Jessica; Wang, Xing; ...

2018-02-23

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discoverymore » that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.« less

The discrimination of automotive clear coats by pyrolysis-gas chromatography/mass spectrometry and comparison of samples by a chromatogram library software.

PubMed

Plage, Bernd; Berg, Anna-Dolores; Luhn, Steven

2008-05-20

The differentiation of 25 automotive clear coats was evaluated using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The samples were selected from eight different groups of samples which slightly differ in their infrared spectra. Most of the samples could be differentiated by visual inspection of the pyrograms. As an objective mean for evaluation a new software based on the comparison of chromatograms was tested for automatic classification considering retention times as well as mass spectra. The database was formed by the triplicate results of the set of the 25 samples. Normally a replicate measurement of a sample yields the best fit by library search. In addition, for most groups classification with moderate fits are obtained for samples belonging to the same group. Some samples are completely rearranged forming a new group of similar samples containing five samples from three different IR groups and four samples of three other groups, respectively. Furthermore detailed visual recognition of individual pyrolysis products allows subgrouping. Therefore, most samples can be differentiated from each other by Py-GC/MS. The exception were three sample groups containing two samples each, which could not be differentiated from each other neither by library search nor by recognition of minor individual pyrolysis products.

GrammarViz 3.0: Interactive Discovery of Variable-Length Time Series Patterns

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

Senin, Pavel; Lin, Jessica; Wang, Xing

The problems of recurrent and anomalous pattern discovery in time series, e.g., motifs and discords, respectively, have received a lot of attention from researchers in the past decade. However, since the pattern search space is usually intractable, most existing detection algorithms require that the patterns have discriminative characteristics and have its length known in advance and provided as input, which is an unreasonable requirement for many real-world problems. In addition, patterns of similar structure, but of different lengths may co-exist in a time series. In order to address these issues, we have developed algorithms for variable-length time series pattern discoverymore » that are based on symbolic discretization and grammar inference—two techniques whose combination enables the structured reduction of the search space and discovery of the candidate patterns in linear time. In this work, we present GrammarViz 3.0—a software package that provides implementations of proposed algorithms and graphical user interface for interactive variable-length time series pattern discovery. The current version of the software provides an alternative grammar inference algorithm that improves the time series motif discovery workflow, and introduces an experimental procedure for automated discretization parameter selection that builds upon the minimum cardinality maximum cover principle and aids the time series recurrent and anomalous pattern discovery.« less

Coexistence of Named Data Networking (NDN) and Software-Defined Networking (SDN)

DTIC Science & Technology

2017-09-01

Networking (NDN) and Software-Defined Networking (SDN) by Vinod Mishra Computational and Information Sciences Directorate, ARL...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching...existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection information . Send comments regarding this

Are There Hidden Supernovae?

NASA Technical Reports Server (NTRS)

Bregman, Jesse; Harker, David; Dunham, E.; Rank, David; Temi, Pasquale

1997-01-01

Ames Research Center and UCSC have been working on the development of a Mid IR Camera for the KAO in order to search for extra galactic supernovae. The development of the camera and its associated data reduction software have been successfully completed. Spectral Imaging of the Orion Bar at 6.2 and 7.8 microns demonstrates the derotation and data reduction software which was developed.

Enabling Interoperability - Supporting a Diversity of Search Paradigms Using Shared Ontologies and Federated Registries

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Crichton, D. J.; Hardman, S. H.; Mattman, C. A.; Ramirez, P. M.

2009-12-01

Experience suggests that no single search paradigm will meet all of a community’s search requirements. Traditional forms based search is still considered critical by a significant percentage of most science communities. However text base and facet based search are improving the community’s perception that search can be easy and that the data is available and can be located. Finally semantic search promises ways to find data that were not conceived when the metadata was first captured and organized. This situation suggests that successful science information systems must be able to deploy new search applications quickly, efficiently, and often for ad-hoc purposes. Federated registries allow data to be packaged or associated with their metadata and managed as simple registry objects. Standard reference models for federated registries now exist that ensure registry objects are uniquely identified at registration and that versioning, classification, and cataloging are addressed automatically. Distributed but locally governed, federated registries also provide notification of registry events and federated query, linking, and replication of registry objects. Key principles for shared ontology development in the space sciences are that the ontology remains independent of its implementation and be extensible, flexible and scalable. The dichotomy between digital things and physical/conceptual things in the domain need to be unified under a standard model, such as the Open Archive Information System (OAIS) Information Object. Finally the fact must be accepted that ontology development is a difficult task that requires time, patience and experts in both the science domain and information modeling. The Planetary Data System (PDS) has adopted this architecture for it next generation information system, PDS 2010. The authors will report on progress, briefly describe key elements, and illustrate how the new system will be phased into operations to handle both legacy and new science data. In particular the shared ontology is being used to drive system implementation through the generation of standards documents and software configuration files. The resulting information system will help meet the expectations of modern scientists by providing more of the information interconnectedness, correlative science, and system interoperability that they desire. Fig.1 - Data Driven Architecture

Multicriteria analysis of ontologically represented information

NASA Astrophysics Data System (ADS)

Wasielewska, K.; Ganzha, M.; Paprzycki, M.; Bǎdicǎ, C.; Ivanovic, M.; Lirkov, I.

2014-11-01

Our current work concerns the development of a decision support system for the software selection problem. The main idea is to utilize expert knowledge to help the user in selecting the best software / method / computational resource to solve a computational problem. Obviously, this involves multicriterial decision making and the key open question is: which method to choose. The context of the work is provided by the Agents in Grid (AiG) project, where the software selection (and thus multicriterial analysis) is to be realized when all information concerning the problem, the hardware and the software is ontologically represented. Initially, we have considered the Analytical Hierarchy Process (AHP), which is well suited for the hierarchical data structures (e.g., such that have been formulated in terms of ontologies). However, due to its well-known shortcomings, we have decided to extend our search for the multicriterial analysis method best suited for the problem in question. In this paper we report results of our search, which involved: (i) TOPSIS (Technique for Order Preference by Similarity to Ideal Solution), (ii) PROMETHEE, and (iii) GRIP (Generalized Regression with Intensities of Preference). We also briefly argue why other methods have not been considered as valuable candidates.

PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences.

PubMed

Ferro, Myriam; Tardif, Marianne; Reguer, Erwan; Cahuzac, Romain; Bruley, Christophe; Vermat, Thierry; Nugues, Estelle; Vigouroux, Marielle; Vandenbrouck, Yves; Garin, Jérôme; Viari, Alain

2008-05-01

PepLine is a fully automated software which maps MS/MS fragmentation spectra of trypsic peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) obtained from partial interpretation of QTOF MS/MS spectra (first module). PSTs are then mapped on the six-frame translations of genomic sequences (second module) giving hits. Hits are then clustered to detect potential coding regions (third module). Our work aimed at optimizing the algorithms of each component to allow the whole pipeline to proceed in a fully automated manner using raw nucleic acid sequences (i.e., genomes that have not been "reduced" to a database of ORFs or putative exons sequences). The whole pipeline was tested on controlled MS/MS spectra sets from standard proteins and from Arabidopsis thaliana envelope chloroplast samples. Our results demonstrate that PepLine competed with protein database searching softwares and was fast enough to potentially tackle large data sets and/or high size genomes. We also illustrate the potential of this approach for the detection of the intron/exon structure of genes.

Tool for Analysis and Reduction of Scientific Data

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

The Automated Scheduling and Planning Environment (ASPEN) computer program has been updated to version 3.0. ASPEN as a whole (up to version 2.0) has been summarized, and selected aspects of ASPEN have been discussed in several previous NASA Tech Briefs articles. Restated briefly, ASPEN is a modular, reconfigurable, application software framework for solving batch problems that involve reasoning about time, activities, states, and resources. Applications of ASPEN can include planning spacecraft missions, scheduling of personnel, and managing supply chains, inventories, and production lines. ASPEN 3.0 can be customized for a wide range of applications and for a variety of computing environments that include various central processing units and randomaccess memories. Domain-specific reasoning modules (e.g., modules for determining orbits for spacecraft) can easily be plugged into ASPEN 3.0. Improvements over other, similar software that have been incorporated into ASPEN 3.0 include a provision for more expressive time-line values, new parsing capabilities afforded by an ASPEN language based on Extensible Markup Language, improved search capabilities, and improved interfaces to other, utility-type software (notably including MATLAB).

Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale

PubMed Central

Durbin, Kenneth R.; Tran, John C.; Zamdborg, Leonid; Sweet, Steve M. M.; Catherman, Adam D.; Lee, Ji Eun; Li, Mingxi; Kellie, John F.; Kelleher, Neil L.

2011-01-01

Applying high-throughput Top-Down MS to an entire proteome requires a yet-to-be-established model for data processing. Since Top-Down is becoming possible on a large scale, we report our latest software pipeline dedicated to capturing the full value of intact protein data in automated fashion. For intact mass detection, we combine algorithms for processing MS1 data from both isotopically resolved (FT) and charge-state resolved (ion trap) LC-MS data, which are then linked to their fragment ions for database searching using ProSight. Automated determination of human keratin and tubulin isoforms is one result. Optimized for the intricacies of whole proteins, new software modules visualize proteome-scale data based on the LC retention time and intensity of intact masses and enable selective detection of PTMs to automatically screen for acetylation, phosphorylation, and methylation. Software functionality was demonstrated using comparative LC-MS data from yeast strains in addition to human cells undergoing chemical stress. We further these advances as a key aspect of realizing Top-Down MS on a proteomic scale. PMID:20848673

Software-Enabled Distributed Network Governance: The PopMedNet Experience.

PubMed

Davies, Melanie; Erickson, Kyle; Wyner, Zachary; Malenfant, Jessica; Rosen, Rob; Brown, Jeffrey

2016-01-01

The expanded availability of electronic health information has led to increased interest in distributed health data research networks. The distributed research network model leaves data with and under the control of the data holder. Data holders, network coordinating centers, and researchers have distinct needs and challenges within this model. The concerns of network stakeholders are addressed in the design and governance models of the PopMedNet software platform. PopMedNet features include distributed querying, customizable workflows, and auditing and search capabilities. Its flexible role-based access control system enables the enforcement of varying governance policies. Four case studies describe how PopMedNet is used to enforce network governance models. Trust is an essential component of a distributed research network and must be built before data partners may be willing to participate further. The complexity of the PopMedNet system must be managed as networks grow and new data, analytic methods, and querying approaches are developed. The PopMedNet software platform supports a variety of network structures, governance models, and research activities through customizable features designed to meet the needs of network stakeholders.

The Raptor Real-Time Processing Architecture

NASA Astrophysics Data System (ADS)

Galassi, M.; Starr, D.; Wozniak, P.; Brozdin, K.

The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback, etc.) is implemented with a ``component'' approach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally, the Raptor architecture is entirely based on free software (sometimes referred to as ``open source'' software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

Raptor -- Mining the Sky in Real Time

NASA Astrophysics Data System (ADS)

Galassi, M.; Borozdin, K.; Casperson, D.; McGowan, K.; Starr, D.; White, R.; Wozniak, P.; Wren, J.

2004-06-01

The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback...) is implemented with a ``component'' aproach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally: the Raptor architecture is entirely based on free software (sometimes referred to as "open source" software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

Real time imaging and infrared background scene analysis using the Naval Postgraduate School infrared search and target designation (NPS-IRSTD) system

NASA Astrophysics Data System (ADS)

Bernier, Jean D.

1991-09-01

The imaging in real time of infrared background scenes with the Naval Postgraduate School Infrared Search and Target Designation (NPS-IRSTD) System was achieved through extensive software developments in protected mode assembly language on an Intel 80386 33 MHz computer. The new software processes the 512 by 480 pixel images directly in the extended memory area of the computer where the DT-2861 frame grabber memory buffers are mapped. Direct interfacing, through a JDR-PR10 prototype card, between the frame grabber and the host computer AT bus enables each load of the frame grabber memory buffers to be effected under software control. The protected mode assembly language program can refresh the display of a six degree pseudo-color sector in the scanner rotation within the two second period of the scanner. A study of the imaging properties of the NPS-IRSTD is presented with preliminary work on image analysis and contrast enhancement of infrared background scenes.

Schroedinger’s code: Source code availability and transparency in astrophysics

NASA Astrophysics Data System (ADS)

Ryan, PW; Allen, Alice; Teuben, Peter

2018-01-01

Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

EndNote 7.0.

PubMed

Eapen, Bell Raj

2006-01-01

EndNote is a useful software for online literature search and efficient bibliography management. It helps to format the bibliography according to the citation style of each journal. EndNote stores references in a library file, which can be shared with others. It can connect to online resources like PubMed and retrieve search results as per the search criteria. It can also effortlessly integrate with popular word processors like MS Word. The Indian Journal of Dermatology, Venereology and Leprology website has a provision to import references to EndNote.

Distributed optimization system and method

DOEpatents

Hurtado, John E.; Dohrmann, Clark R.; Robinett, III, Rush D.

2003-06-10

A search system and method for controlling multiple agents to optimize an objective using distributed sensing and cooperative control. The search agent can be one or more physical agents, such as a robot, and can be software agents for searching cyberspace. The objective can be: chemical sources, temperature sources, radiation sources, light sources, evaders, trespassers, explosive sources, time dependent sources, time independent sources, function surfaces, maximization points, minimization points, and optimal control of a system such as a communication system, an economy, a crane, and a multi-processor computer.

Distributed Optimization System

DOEpatents

Hurtado, John E.; Dohrmann, Clark R.; Robinett, III, Rush D.

2004-11-30

A search system and method for controlling multiple agents to optimize an objective using distributed sensing and cooperative control. The search agent can be one or more physical agents, such as a robot, and can be software agents for searching cyberspace. The objective can be: chemical sources, temperature sources, radiation sources, light sources, evaders, trespassers, explosive sources, time dependent sources, time independent sources, function surfaces, maximization points, minimization points, and optimal control of a system such as a communication system, an economy, a crane, and a multi-processor computer.

The ESGF Software Stack: a Configurable and Extensible Framework for Enabling Access to Geospatial Data

NASA Astrophysics Data System (ADS)

Cinquini, L.; Bell, G. M.; Williams, D.; Harney, J.

2012-12-01

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing state-of-the-art services for the management and access of Earth system data. ESGF is currently used to serve the totality of the model output used for the forthcoming IPCC 5th assessment report on climate change, as well as supporting observational and reanalysis datasets. Also, it is been adopted by several other projects that focus on global, regional and local climate modeling. The ESGF software stack is composed of several modular applications that cover related but disjoint areas of functionality: data publishing, data search and discovery, data access, user management, security, and federation. Overall, the ESGF infrastructure offers a configurable end-to-end solution to the problem of enabling web-based access to large amounts of geospatial data. This talk will present the architectural and configuration options that are available to a data provider leveraging ESGF to serve their data: which services to expose, how to scale to larger data collections, how to establish access control, how to customize the user interface, and others. Additionally, the framework provides extension points that allow each site to plug in custom functionality such as crawling of specific metadata repositories, exposing domain-specific analysis and visualization services, developing custom access clients that interact with the system APIs. These configuration and extension capabilities are based on simple but effective domain-specific object models, that underpin the software applications: the data model, the security model, and the federation model. The ESGF software stack is developed collaboratively by software engineers at many institutions around the world, and is made freely available to the community under an open source license to promote adoption, reuse, inspection and continuous improvement.

[Search for potential gastric cancer biomarkers using low molecular weight blood plasma proteome profiling by mass spectrometry].

PubMed

Shevchenko, V E; Arnotskaia, N E; Ogorodnikova, E V; Davydov, M M; Ibraev, M A; Turkin, I N; Davydov, M I

2014-01-01

Gastric cancer, one of the most widespread malignant tumors, still lacks reliable serum/plasma biomarkers of its early detection. In this study we have developed, unified, and tested a new methodology for search of gastric cancer biomarkers based on profiling of low molecular weight proteome (LMWP) (1-17 kDa). This approach included three main components: sample pre-fractionation, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS), data analysis by a bioinformatics software package. Applicability and perspectives of the developed approach for detection of potential gastric cancer markers during LMWP analysis have been demonstrated using 69 plasma samples from patients with gastric cancer (stages I-IV) and 238 control samples. The study revealed peptides/polypeptides, which may be potentially used for detection of this pathology.

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design

PubMed Central

Pan, Yuchao; Dong, Yuxi; Zhou, Jingtian; Hallen, Mark; Donald, Bruce R.; Xu, Wei

2016-01-01

Abstract Finding the global minimum energy conformation (GMEC) of a huge combinatorial search space is the key challenge in computational protein design (CPD) problems. Traditional algorithms lack a scalable and efficient distributed design scheme, preventing researchers from taking full advantage of current cloud infrastructures. We design cloud OSPREY (cOSPREY), an extension to a widely used protein design software OSPREY, to allow the original design framework to scale to the commercial cloud infrastructures. We propose several novel designs to integrate both algorithm and system optimizations, such as GMEC-specific pruning, state search partitioning, asynchronous algorithm state sharing, and fault tolerance. We evaluate cOSPREY on three different cloud platforms using different technologies and show that it can solve a number of large-scale protein design problems that have not been possible with previous approaches. PMID:27154509

Computer assisted analysis of auroral images obtained from high altitude polar satellites

NASA Technical Reports Server (NTRS)

Samadani, Ramin; Flynn, Michael

1993-01-01

Automatic techniques that allow the extraction of physically significant parameters from auroral images were developed. This allows the processing of a much larger number of images than is currently possible with manual techniques. Our techniques were applied to diverse auroral image datasets. These results were made available to geophysicists at NASA and at universities in the form of a software system that performs the analysis. After some feedback from users, an upgraded system was transferred to NASA and to two universities. The feasibility of user-trained search and retrieval of large amounts of data using our automatically derived parameter indices was demonstrated. Techniques based on classification and regression trees (CART) were developed and applied to broaden the types of images to which the automated search and retrieval may be applied. Our techniques were tested with DE-1 auroral images.

An engineering approach to automatic programming

NASA Technical Reports Server (NTRS)

Rubin, Stuart H.

1990-01-01

An exploratory study of the automatic generation and optimization of symbolic programs using DECOM - a prototypical requirement specification model implemented in pure LISP was undertaken. It was concluded, on the basis of this study, that symbolic processing languages such as LISP can support a style of programming based upon formal transformation and dependent upon the expression of constraints in an object-oriented environment. Such languages can represent all aspects of the software generation process (including heuristic algorithms for effecting parallel search) as dynamic processes since data and program are represented in a uniform format.

MECH: Algorithms and Tools for Automated Assessment of Potential Attack Locations (Software User Guide)

DTIC Science & Technology

2015-10-02

hour per response, including the time for reviewing instructions, searching existing data sources , gathering and maintaining the data needed, and...architecture of MECH v0.1 is shown in Figure 1. The Android MECH-App shown on the left side of the figure is for end users to request tactical risk...when or where the next attack will take place.   3    2 MECH-App MECH-App runs on a touch screen based Android device for end users to access the

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.

PubMed

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J; Ball, Catherine A

2010-10-01

Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows.

Agile: From Software to Mission System

NASA Technical Reports Server (NTRS)

Trimble, Jay; Shirley, Mark H.; Hobart, Sarah Groves

2016-01-01

The Resource Prospector (RP) is an in-situ resource utilization (ISRU) technology demonstration mission, designed to search for volatiles at the Lunar South Pole. This is NASA's first near real time tele-operated rover on the Moon. The primary objective is to search for volatiles at one of the Lunar Poles. The combination of short mission duration, a solar powered rover, and the requirement to explore shadowed regions makes for an operationally challenging mission. To maximize efficiency and flexibility in Mission System design and thus to improve the performance and reliability of the resulting Mission System, we are tailoring Agile principles that we have used effectively in ground data system software development and applying those principles to the design of elements of the mission operations system.

A survey of the current status of web-based databases indexing Iranian journals.

PubMed

Merat, Shahin; Khatibzadeh, Shahab; Mesgarpour, Bita; Malekzadeh, Reza

2009-05-01

The scientific output of Iran is increasing rapidly during the recent years. Unfortunately, most papers are published in journals which are not indexed by popular indexing systems and many of them are in Persian without English translation. This makes the results of Iranian scientific research unavailable to other researchers, including Iranians. The aim of this study was to evaluate the quality of current web-based databases indexing scientific articles published in Iran. We identified web-based databases which indexed scientific journals published in Iran using popular search engines. The sites were then subjected to a series of tests to evaluate their coverage, search capabilities, stability, accuracy of information, consistency, accessibility, ease of use, and other features. Results were compared with each other to identify strengths and shortcomings of each site. Five web sites were indentified. None had a complete coverage on scientific Iranian journals. The search capabilities were less than optimal in most sites. English translations of research titles, author names, keywords, and abstracts of Persian-language articles did not follow standards. Some sites did not cover abstracts. Numerous typing errors make searches ineffective and citation indexing unreliable. None of the currently available indexing sites are capable of presenting Iranian research to the international scientific community. The government should intervene by enforcing policies designed to facilitate indexing through a systematic approach. The policies should address Iranian journals, authors, and indexing sites. Iranian journals should be required to provide their indexing data, including references, electronically; authors should provide correct indexing information to journals; and indexing sites should improve their software to meet standards set by the government.

Judicious use of custom development in an open source component architecture

NASA Astrophysics Data System (ADS)

Bristol, S.; Latysh, N.; Long, D.; Tekell, S.; Allen, J.

2014-12-01

Modern software engineering is not as much programming from scratch as innovative assembly of existing components. Seamlessly integrating disparate components into scalable, performant architecture requires sound engineering craftsmanship and can often result in increased cost efficiency and accelerated capabilities if software teams focus their creativity on the edges of the problem space. ScienceBase is part of the U.S. Geological Survey scientific cyberinfrastructure, providing data and information management, distribution services, and analysis capabilities in a way that strives to follow this pattern. ScienceBase leverages open source NoSQL and relational databases, search indexing technology, spatial service engines, numerous libraries, and one proprietary but necessary software component in its architecture. The primary engineering focus is cohesive component interaction, including construction of a seamless Application Programming Interface (API) across all elements. The API allows researchers and software developers alike to leverage the infrastructure in unique, creative ways. Scaling the ScienceBase architecture and core API with increasing data volume (more databases) and complexity (integrated science problems) is a primary challenge addressed by judicious use of custom development in the component architecture. Other data management and informatics activities in the earth sciences have independently resolved to a similar design of reusing and building upon established technology and are working through similar issues for managing and developing information (e.g., U.S. Geoscience Information Network; NASA's Earth Observing System Clearing House; GSToRE at the University of New Mexico). Recent discussions facilitated through the Earth Science Information Partners are exploring potential avenues to exploit the implicit relationships between similar projects for explicit gains in our ability to more rapidly advance global scientific cyberinfrastructure.

WebDASC: a web-based dietary assessment software for 8-11-year-old Danish children.

PubMed

Biltoft-Jensen, A; Trolle, E; Christensen, T; Islam, N; Andersen, L F; Egenfeldt-Nielsen, S; Tetens, I

2014-01-01

  The present study describes the development and formative evaluation of the Web-based Dietary Assessment Software for Children (WebDASC). WebDASC is part of the OPUS project ('Optimal well-being, development and health for Danish children through a healthy New Nordic Diet') and was intended to measure dietary change resulting from a school-based intervention.   WebDASC was developed as a self-administered tool that could be used by 8-11-year-old children with or without parent's aid. The development of WebDASC followed a prototyping approach: focus groups, informal interviews, literature review, and usability tests preceded its release. Special consideration was given to age-appropriate design issues.   In WebDASC an animated armadillo guides respondents through six daily eating occasions and helps them report foods and beverages previously consumed. A database of 1300 food items is available either through category browse or free text search, aided by a spell check application. A type-in format is available for foods not otherwise found through category browse or text search. Amount consumed is estimated by selecting the closest portion size among four different digital images. WebDASC includes internal checks for frequently forgotten foods, and the following features to create motivation: a food-meter displaying cumulative weight of foods reported, a most popular food ranking, and a computer game with a high score list.   WebDASC was developed as an intuitive, cost-effective, and engaging method to collect detailed dietary data from 8- to 11-year-old children. Preliminary testing demonstrated that it was well accepted among children. © 2012 The Authors. Journal of Human Nutrition and Dietetics © 2012 The British Dietetic Association Ltd.

A collection of open source applications for mass spectrometry data mining.

PubMed

Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

2014-10-01

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluating the solution from MrBUMP and BALBES

PubMed Central

Keegan, Ronan M.; Long, Fei; Fazio, Vincent J.; Winn, Martyn D.; Murshudov, Garib N.; Vagin, Alexei A.

2011-01-01

Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software. PMID:21460449

Virtual Boutique: a 3D modeling and content-based management approach to e-commerce

NASA Astrophysics Data System (ADS)

Paquet, Eric; El-Hakim, Sabry F.

2000-12-01

The Virtual Boutique is made out of three modules: the decor, the market and the search engine. The decor is the physical space occupied by the Virtual Boutique. It can reproduce any existing boutique. For this purpose, photogrammetry is used. A set of pictures of a real boutique or space is taken and a virtual 3D representation of this space is calculated from them. Calculations are performed with software developed at NRC. This representation consists of meshes and texture maps. The camera used in the acquisition process determines the resolution of the texture maps. Decorative elements are added like painting, computer generated objects and scanned objects. The objects are scanned with laser scanner developed at NRC. This scanner allows simultaneous acquisition of range and color information based on white laser beam triangulation. The second module, the market, is made out of all the merchandises and the manipulators, which are used to manipulate and compare the objects. The third module, the search engine, can search the inventory based on an object shown by the customer in order to retrieve similar objects base don shape and color. The items of interest are displayed in the boutique by reconfiguring the market space, which mean that the boutique can be continuously customized according to the customer's needs. The Virtual Boutique is entirely written in Java 3D and can run in mono and stereo mode and has been optimized in order to allow high quality rendering.

National Geothermal Data System: Open Access to Geoscience Data, Maps, and Documents

NASA Astrophysics Data System (ADS)

Caudill, C. M.; Richard, S. M.; Musil, L.; Sonnenschein, A.; Good, J.

2014-12-01

The U.S. National Geothermal Data System (NGDS) provides free open access to millions of geoscience data records, publications, maps, and reports via distributed web services to propel geothermal research, development, and production. NGDS is built on the US Geoscience Information Network (USGIN) data integration framework, which is a joint undertaking of the USGS and the Association of American State Geologists (AASG), and is compliant with international standards and protocols. NGDS currently serves geoscience information from 60+ data providers in all 50 states. Free and open source software is used in this federated system where data owners maintain control of their data. This interactive online system makes geoscience data easily discoverable, accessible, and interoperable at no cost to users. The dynamic project site http://geothermaldata.org serves as the information source and gateway to the system, allowing data and applications discovery and availability of the system's data feed. It also provides access to NGDS specifications and the free and open source code base (on GitHub), a map-centric and library style search interface, other software applications utilizing NGDS services, NGDS tutorials (via YouTube and USGIN site), and user-created tools and scripts. The user-friendly map-centric web-based application has been created to support finding, visualizing, mapping, and acquisition of data based on topic, location, time, provider, or key words. Geographic datasets visualized through the map interface also allow users to inspect the details of individual GIS data points (e.g. wells, geologic units, etc.). In addition, the interface provides the information necessary for users to access the GIS data from third party software applications such as GoogleEarth, UDig, and ArcGIS. A redistributable, free and open source software package called GINstack (USGIN software stack) was also created to give data providers a simple way to release data using interoperable and shareable standards, upload data and documents, and expose those data as a node in the NGDS or any larger data system through a CSW endpoint. The easy-to-use interface is supported by back-end software including Postgres, GeoServer, and custom CKAN extensions among others.

OntoSoft: A Software Registry for Geosciences

NASA Astrophysics Data System (ADS)

Garijo, D.; Gil, Y.

2017-12-01

The goal of the EarthCube OntoSoft project is to enable the creation of an ecosystem for software stewardship in geosciences that will empower scientists to manage their software as valuable scientific assets. By sharing software metadata in OntoSoft, scientists enable broader access to that software by other scientists, software professionals, students, and decision makers. Our work to date includes: 1) an ontology for describing scientific software metadata, 2) a distributed scientific software repository that contains more than 750 entries that can be searched and compared across metadata fields, 3) an intelligent user interface that guides scientists to publish software and allows them to crowdsource its corresponding metadata. We have also developed a training program where scientists learn to describe and cite software in their papers in addition to data and provenance, and we are using OntoSoft to show them the benefits of publishing their software metadata. This training program is part of a Geoscience Papers of the Future Initiative, where scientists are reflecting on their current practices, benefits and effort for sharing software and data. This journal paper can be submitted to a Special Section of the AGU Earth and Space Science Journal.

MIL3DAE

Atmospheric Science Data Center

2018-04-19

... Earthdata Search   Parameters:  Average aerosol optical depth Order Data:  MISR Order Tool:  Order ... Readme Files:  Processing Status:  Aerosol/Land Production Report:  Daily Read Software ...

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

PubMed

Colak, Recep; Moser, Flavia; Chu, Jeffrey Shih-Chieh; Schönhuth, Alexander; Chen, Nansheng; Ester, Martin

2010-10-25

Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large-scale datasets. Software and data sets are available at http://www.sfu.ca/~ester/software/DECOB.zip.

STARS 2.0: 2nd-generation open-source archiving and query software

NASA Astrophysics Data System (ADS)

Winegar, Tom

2008-07-01

The Subaru Telescope is in process of developing an open-source alternative to the 1st-generation software and databases (STARS 1) used for archiving and query. For STARS 2, we have chosen PHP and Python for scripting and MySQL as the database software. We have collected feedback from staff and observers, and used this feedback to significantly improve the design and functionality of our future archiving and query software. Archiving - We identified two weaknesses in 1st-generation STARS archiving software: a complex and inflexible table structure and uncoordinated system administration for our business model: taking pictures from the summit and archiving them in both Hawaii and Japan. We adopted a simplified and normalized table structure with passive keyword collection, and we are designing an archive-to-archive file transfer system that automatically reports real-time status and error conditions and permits error recovery. Query - We identified several weaknesses in 1st-generation STARS query software: inflexible query tools, poor sharing of calibration data, and no automatic file transfer mechanisms to observers. We are developing improved query tools and sharing of calibration data, and multi-protocol unassisted file transfer mechanisms for observers. In the process, we have redefined a 'query': from an invisible search result that can only transfer once in-house right now, with little status and error reporting and no error recovery - to a stored search result that can be monitored, transferred to different locations with multiple protocols, reporting status and error conditions and permitting recovery from errors.

Identification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus.

PubMed

Lu, Lei; Millikin, Robert J; Solntsev, Stefan K; Rolfs, Zach; Scalf, Mark; Shortreed, Michael R; Smith, Lloyd M

2018-05-25

Protein chemical crosslinking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of crosslinkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of crosslinked proteins are still in need. Here we report MetaMorpheusXL, a new search module within the MetaMorpheus software suite that identifies both MS-cleavable and non-cleavable crosslinked peptides in MS data. MetaMorpheusXL identifies MS-cleavable crosslinked peptides with an ion-indexing algorithm, which enables an efficient large database search. The identification does not require the presence of signature fragment ions, an advantage compared to similar programs such as XlinkX. One complication associated with the need for signature ions from cleavable crosslinkers such as DSSO (disuccinimidyl sulfoxide) is the requirement for multiple fragmentation types and energy combinations, which is not necessary for MetaMorpheusXL. The ability to perform proteome-wide analysis is another advantage of MetaMorpheusXl compared to such programs as MeroX and DXMSMS. MetaMorpheusXL is also faster than other currently available MS-cleavable crosslink search software programs. It is imbedded in MetaMorpheus, an open-source and freely available software suite that provides a reliable, fast, user-friendly graphical user interface that is readily accessible to researchers.

Automated extraction of chemical structure information from digital raster images

PubMed Central

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

RTECS database (on the internet). Online data

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

NONE

The Registry of Toxic Effects of Chemical Substances (RTECS (trademark)) is a database of toxicological information compiled, maintained, and updated by the National Institute for Occupational Safety and Health. The program is mandated by the Occupational Safety and Health Act of 1970. The original edition, known as the `Toxic Substances List,` was published on June 28, 1971, and included toxicologic data for approximately 5,000 chemicals. Since that time, the list has continuously grown and been updated, and its name changed to the current title, `Registry of Toxic Effects of Chemical Substances.` RTECS (trademark) now contains over 133,000 chemicals as NIOSHmore » strives to fulfill the mandate to list `all known toxic substances...and the concentrations at which...toxicity is known to occur.` This database is now available for searching through the Gov. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

VisEL: Visualisation of Expertise Level in a Special Interest Group Knowledge Portal

NASA Astrophysics Data System (ADS)

Zulhafizsyam Wan Ahmad, Wan Muhammad; Sulaiman, Shahida; Yusof, Umi Kalsom

A variety of portals are available nowadays to support diverse purposes such as commercial, publishing, personal, affinity and corporate portals. Affinity portals promote electronic communities who share common interest such as a special interest group (SIG). Knowledge portal is an emerging trend that benefits the existing portal technology by designing such portals with proper representation of the members' shared knowledge. Besides textual representation for diverse expertise levels, graphical visualisation will be able to support the requirements in searching and representing expertise level among e-community. There is a number of existing SIG portals available. However, they do not visualise effectively and accurately the expertise level of members and make it difficult for users to search their targeted experts for instance searching the highest expertise level to have a discussion and to solve their problems related to a project. The goal of this paper is to propose a graphical visualisation of expertise level method (VisEL) using an interactive tag cloud technique that represents expertise level of each member based on their knowledge in a software engineering SIG portal.

Using C to build a satellite scheduling expert system: Examples from the Explorer platform planning system

NASA Technical Reports Server (NTRS)

Mclean, David R.; Tuchman, Alan; Potter, William J.

1991-01-01

Recently, many expert systems were developed in a LISP environment and then ported to the real world C environment before the final system is delivered. This situation may require that the entire system be completely rewritten in C and may actually result in a system which is put together as quickly as possible with little regard for maintainability and further evolution. With the introduction of high performance UNIX and X-windows based workstations, a great deal of the advantages of developing a first system in the LISP environment have become questionable. A C-based AI development effort is described which is based on a software tools approach with emphasis on reusability and maintainability of code. The discussion starts with simple examples of how list processing can easily be implemented in C and then proceeds to the implementations of frames and objects which use dynamic memory allocation. The implementation of procedures which use depth first search, constraint propagation, context switching and a blackboard-like simulation environment are described. Techniques for managing the complexity of C-based AI software are noted, especially the object-oriented techniques of data encapsulation and incremental development. Finally, all these concepts are put together by describing the components of planning software called the Planning And Resource Reasoning (PARR) shell. This shell was successfully utilized for scheduling services of the Tracking and Data Relay Satellite System for the Earth Radiation Budget Satellite since May 1987 and will be used for operations scheduling of the Explorer Platform in November 1991.

NASA Tech Briefs, March 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics covered include: Scheme for Entering Binary Data Into a Quantum Computer; Encryption for Remote Control via Internet or Intranet; Coupled Receiver/Decoders for Low-Rate Turbo Codes; Processing GPS Occultation Data To Characterize Atmosphere; Displacing Unpredictable Nulls in Antenna Radiation Patterns; Integrated Pointing and Signal Detector for Optical Receiver; Adaptive Thresholding and Parameter Estimation for PPM; Data-Driven Software Framework for Web-Based ISS Telescience; Software for Secondary-School Learning About Robotics; Fuzzy Logic Engine; Telephone-Directory Program; Simulating a Direction-Finder Search for an ELT; Formulating Precursors for Coating Metals and Ceramics; Making Macroscopic Assemblies of Aligned Carbon Nanotubes; Ball Bearings Equipped for In Situ Lubrication on Demand; Synthetic Bursae for Robots; Robot Forearm and Dexterous Hand; Making a Metal-Lined Composite-Overwrapped Pressure Vessel; Ex Vivo Growth of Bioengineered Ligaments and Other Tissues; Stroboscopic Goggles for Reduction of Motion Sickness; Articulating Support for Horizontal Resistive Exercise; Modified Penning-Malmberg Trap for Storing Antiprotons; Tumbleweed Rovers; Two-Photon Fluorescence Microscope for Microgravity Research; Biased Randomized Algorithm for Fast Model-Based Diagnosis; Fast Algorithms for Model-Based Diagnosis; Simulations of Evaporating Multicomponent Fuel Drops; Formation Flying of Tethered and Nontethered Spacecraft; and Two Methods for Efficient Solution of the Hitting- Set Problem.

Use of a data warehouse at an academic medical center for clinical pathology quality improvement, education, and research

PubMed Central

Krasowski, Matthew D.; Schriever, Andy; Mathur, Gagan; Blau, John L.; Stauffer, Stephanie L.; Ford, Bradley A.

2015-01-01

Background: Pathology data contained within the electronic health record (EHR), and laboratory information system (LIS) of hospitals represents a potentially powerful resource to improve clinical care. However, existing reporting tools within commercial EHR and LIS software may not be able to efficiently and rapidly mine data for quality improvement and research applications. Materials and Methods: We present experience using a data warehouse produced collaboratively between an academic medical center and a private company. The data warehouse contains data from the EHR, LIS, admission/discharge/transfer system, and billing records and can be accessed using a self-service data access tool known as Starmaker. The Starmaker software allows users to use complex Boolean logic, include and exclude rules, unit conversion and reference scaling, and value aggregation using a straightforward visual interface. More complex queries can be achieved by users with experience with Structured Query Language. Queries can use biomedical ontologies such as Logical Observation Identifiers Names and Codes and Systematized Nomenclature of Medicine. Result: We present examples of successful searches using Starmaker, falling mostly in the realm of microbiology and clinical chemistry/toxicology. The searches were ones that were either very difficult or basically infeasible using reporting tools within the EHR and LIS used in the medical center. One of the main strengths of Starmaker searches is rapid results, with typical searches covering 5 years taking only 1–2 min. A “Run Count” feature quickly outputs the number of cases meeting criteria, allowing for refinement of searches before downloading patient-identifiable data. The Starmaker tool is available to pathology residents and fellows, with some using this tool for quality improvement and scholarly projects. Conclusion: A data warehouse has significant potential for improving utilization of clinical pathology testing. Software that can access data warehouse using a straightforward visual interface can be incorporated into pathology training programs. PMID:26284156

Use of a data warehouse at an academic medical center for clinical pathology quality improvement, education, and research.

PubMed

Krasowski, Matthew D; Schriever, Andy; Mathur, Gagan; Blau, John L; Stauffer, Stephanie L; Ford, Bradley A

2015-01-01

Pathology data contained within the electronic health record (EHR), and laboratory information system (LIS) of hospitals represents a potentially powerful resource to improve clinical care. However, existing reporting tools within commercial EHR and LIS software may not be able to efficiently and rapidly mine data for quality improvement and research applications. We present experience using a data warehouse produced collaboratively between an academic medical center and a private company. The data warehouse contains data from the EHR, LIS, admission/discharge/transfer system, and billing records and can be accessed using a self-service data access tool known as Starmaker. The Starmaker software allows users to use complex Boolean logic, include and exclude rules, unit conversion and reference scaling, and value aggregation using a straightforward visual interface. More complex queries can be achieved by users with experience with Structured Query Language. Queries can use biomedical ontologies such as Logical Observation Identifiers Names and Codes and Systematized Nomenclature of Medicine. We present examples of successful searches using Starmaker, falling mostly in the realm of microbiology and clinical chemistry/toxicology. The searches were ones that were either very difficult or basically infeasible using reporting tools within the EHR and LIS used in the medical center. One of the main strengths of Starmaker searches is rapid results, with typical searches covering 5 years taking only 1-2 min. A "Run Count" feature quickly outputs the number of cases meeting criteria, allowing for refinement of searches before downloading patient-identifiable data. The Starmaker tool is available to pathology residents and fellows, with some using this tool for quality improvement and scholarly projects. A data warehouse has significant potential for improving utilization of clinical pathology testing. Software that can access data warehouse using a straightforward visual interface can be incorporated into pathology training programs.

Model authoring system for fail safe analysis

NASA Technical Reports Server (NTRS)

Sikora, Scott E.

1990-01-01

The Model Authoring System is a prototype software application for generating fault tree analyses and failure mode and effects analyses for circuit designs. Utilizing established artificial intelligence and expert system techniques, the circuits are modeled as a frame-based knowledge base in an expert system shell, which allows the use of object oriented programming and an inference engine. The behavior of the circuit is then captured through IF-THEN rules, which then are searched to generate either a graphical fault tree analysis or failure modes and effects analysis. Sophisticated authoring techniques allow the circuit to be easily modeled, permit its behavior to be quickly defined, and provide abstraction features to deal with complexity.

Improving the efficiency of dissolved oxygen control using an on-line control system based on a genetic algorithm evolving FWNN software sensor.

PubMed

Ruan, Jujun; Zhang, Chao; Li, Ya; Li, Peiyi; Yang, Zaizhi; Chen, Xiaohong; Huang, Mingzhi; Zhang, Tao

2017-02-01

This work proposes an on-line hybrid intelligent control system based on a genetic algorithm (GA) evolving fuzzy wavelet neural network software sensor to control dissolved oxygen (DO) in an anaerobic/anoxic/oxic process for treating papermaking wastewater. With the self-learning and memory abilities of neural network, handling the uncertainty capacity of fuzzy logic, analyzing local detail superiority of wavelet transform and global search of GA, this proposed control system can extract the dynamic behavior and complex interrelationships between various operation variables. The results indicate that the reasonable forecasting and control performances were achieved with optimal DO, and the effluent quality was stable at and below the desired values in real time. Our proposed hybrid approach proved to be a robust and effective DO control tool, attaining not only adequate effluent quality but also minimizing the demand for energy, and is easily integrated into a global monitoring system for purposes of cost management. Copyright © 2016 Elsevier Ltd. All rights reserved.

Knowledge assistant: A sensor fusion framework for robotic environmental characterization

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

Feddema, J.T.; Rivera, J.J.; Tucker, S.D.

1996-12-01

A prototype sensor fusion framework called the {open_quotes}Knowledge Assistant{close_quotes} has been developed and tested on a gantry robot at Sandia National Laboratories. This Knowledge Assistant guides the robot operator during the planning, execution, and post analysis stages of the characterization process. During the planning stage, the Knowledge Assistant suggests robot paths and speeds based on knowledge of sensors available and their physical characteristics. During execution, the Knowledge Assistant coordinates the collection of data through a data acquisition {open_quotes}specialist.{close_quotes} During execution and post analysis, the Knowledge Assistant sends raw data to other {open_quotes}specialists,{close_quotes} which include statistical pattern recognition software, a neuralmore » network, and model-based search software. After the specialists return their results, the Knowledge Assistant consolidates the information and returns a report to the robot control system where the sensed objects and their attributes (e.g. estimated dimensions, weight, material composition, etc.) are displayed in the world model. This paper highlights the major components of this system.« less

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

PubMed

Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

2016-01-01

As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

Interface Between CDS/ISIS and the Web at the Library of the Cagliari Observatory

NASA Astrophysics Data System (ADS)

Mureddu, Leonardo; Denotti, Franca; Alvito, Gianni

The library catalog of the Cagliari Observatory was digitized some years ago, by using CDS/ISIS with a practical format named ``ASTCA'' derived from the well-known ``BIBLO''. Recently the observatory has put some effort into the creation and maintenance of a Web site; on that occasion the library database has been interfaced to the Web server by means of the software WWWISIS and a locally created search form. Both books and journals can be searched by remote users. Book searches can be made by authors, titles or keywords.

Countering Insider Threats - Handling Insider Threats Using Dynamic, Run-Time Forensics

DTIC Science & Technology

2007-10-01

able to handle the security policy requirements of a large organization containing many decentralized and diverse users, while being easily managed... contained in the TIF folder. Searching for any text string and sorting is supported also. The cache index file of Internet Explorer is not changed... containing thousands of malware software signatures. Separate datasets can be created for various classifications of malware such as encryption software

Enabling Software Acquisition Improvement: Government and Industry Software Development Team Acquisition Model

DTIC Science & Technology

2010-04-30

estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources , gathering and maintaining...previous and current complex SW development efforts, the program offices will have a source of objective lessons learned and metrics that can be applied...the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this

The NASA Integrated Vehicle Health Management Technology Experiment for X-37

NASA Technical Reports Server (NTRS)

Schwabacher, Mark; Samuels, Jeff; Brownston, Lee; Clancy, Daniel (Technical Monitor)

2002-01-01

The NASA Integrated Vehicle Health Management (IVHM) Technology Experiment for X-37 was intended to run IVHM software on-board the X-37 spacecraft. The X-37 is intended to be an unpiloted vehicle that would orbit the Earth for up to 21 days before landing on a runway. The objectives of the experiment were to demonstrate the benefits of in-flight IVHM to the operation of a Reusable Launch Vehicle, to advance the Technology Readiness Level of this IVHM technology within a flight environment, and to demonstrate that the IVHM software could operate on the Vehicle Management Computer. The scope of the experiment was to perform real-time fault detection and isolation for X-37's electrical power system and electro-mechanical actuators. The experiment used Livingstone, a software system that performs diagnosis using a qualitative, model-based reasoning approach that searches system-wide interactions to detect and isolate failures. Two of the challenges we faced were to make this research software more efficient so that it would fit within the limited computational resources that were available to us on the X-37 spacecraft, and to modify it so that it satisfied the X-37's software safety requirements. Although the experiment is currently unfunded, the development effort had value in that it resulted in major improvements in Livingstone's efficiency and safety. This paper reviews some of the details of the modeling and integration efforts, and some of the lessons that were learned.

A Tour of Big Data, Open Source Data Management Technologies from the Apache Software Foundation

NASA Astrophysics Data System (ADS)

Mattmann, C. A.

2012-12-01

The Apache Software Foundation, a non-profit foundation charged with dissemination of open source software for the public good, provides a suite of data management technologies for distributed archiving, data ingestion, data dissemination, processing, triage and a host of other functionalities that are becoming critical in the Big Data regime. Apache is the world's largest open source software organization, boasting over 3000 developers from around the world all contributing to some of the most pervasive technologies in use today, from the HTTPD web server that powers a majority of Internet web sites to the Hadoop technology that is now projected at over a $1B dollar industry. Apache data management technologies are emerging as de facto off-the-shelf components for searching, distributing, processing and archiving key science data sets both geophysical, space and planetary based, all the way to biomedicine. In this talk, I will give a virtual tour of the Apache Software Foundation, its meritocracy and governance structure, and also its key big data technologies that organizations can take advantage of today and use to save cost, schedule, and resources in implementing their Big Data needs. I'll illustrate the Apache technologies in the context of several national priority projects, including the U.S. National Climate Assessment (NCA), and in the International Square Kilometre Array (SKA) project that are stretching the boundaries of volume, velocity, complexity, and other key Big Data dimensions.

Reconfigurable Transceiver and Software-Defined Radio Architecture and Technology Evaluated for NASA Space Communications

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.

2004-01-01

The NASA Glenn Research Center is investigating the development and suitability of a software-based open-architecture for space-based reconfigurable transceivers (RTs) and software-defined radios (SDRs). The main objectives of this project are to enable advanced operations and reduce mission costs. SDRs are becoming more common because of the capabilities of reconfigurable digital signal processing technologies such as field programmable gate arrays and digital signal processors, which place radio functions in firmware and software that were traditionally performed with analog hardware components. Features of interest of this communications architecture include nonproprietary open standards and application programming interfaces to enable software reuse and portability, independent hardware and software development, and hardware and software functional separation. The goals for RT and SDR technologies for NASA space missions include prelaunch and on-orbit frequency and waveform reconfigurability and programmability, high data rate capability, and overall communications and processing flexibility. These operational advances over current state-of-art transceivers will be provided to reduce the power, mass, and cost of RTs and SDRs for space communications. The open architecture for NASA communications will support existing (legacy) communications needs and capabilities while providing a path to more capable, advanced waveform development and mission concepts (e.g., ad hoc constellations with self-healing networks and high-rate science data return). A study was completed to assess the state of the art in RT architectures, implementations, and technologies. In-house researchers conducted literature searches and analysis, interviewed Government and industry contacts, and solicited information and white papers from industry on space-qualifiable RTs and SDRs and their associated technologies for space-based NASA applications. The white papers were evaluated, compiled, and used to assess RT and SDR system architectures and core technology elements to determine an appropriate investment strategy to advance these technologies to meet future mission needs. The use of these radios in the space environment represents a challenge because of the space radiation suitability of the components, which drastically reduces the processing capability. The radios available for space are considered to be RTs (as opposed to SDRs), which are digitally programmable radios with selectable changes from an architecture combining analog and digital components. The limited flexibility of this design contrasts against the desire to have a power-efficient solution and open architecture.

Complexity: an internet resource for analysis of DNA sequence complexity

PubMed Central

Orlov, Y. L.; Potapov, V. N.

2004-01-01

The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures, as well as by a combination of all these factors. Several numerical measures of textual complexity, including combinatorial and linguistic ones, together with complexity estimation using a modified Lempel–Ziv algorithm, have been implemented in a software tool called ‘Complexity’ (http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/). The software enables a user to search for low-complexity regions in long sequences, e.g. complete bacterial genomes or eukaryotic chromosomes. In addition, it estimates the complexity of groups of aligned sequences. PMID:15215465

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

PubMed Central

Li, Isaac TS; Shum, Warren; Truong, Kevin

2007-01-01

Background To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive. Results In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGA-based hardware that implemented a module for computing the score of a single cell of the SW matrix. Then using a grid of this module, the entire SW matrix was computed at the speed of field propagation through the FPGA circuit. These modifications dramatically accelerated the algorithm's computation time by up to 160 folds compared to a pure software implementation running on the same FPGA with an Altera Nios II softprocessor. Conclusion This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching. PMID:17555593

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA).

PubMed

Li, Isaac T S; Shum, Warren; Truong, Kevin

2007-06-07

To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive. In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGA-based hardware that implemented a module for computing the score of a single cell of the SW matrix. Then using a grid of this module, the entire SW matrix was computed at the speed of field propagation through the FPGA circuit. These modifications dramatically accelerated the algorithm's computation time by up to 160 folds compared to a pure software implementation running on the same FPGA with an Altera Nios II softprocessor. This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching.

Proposal for a telehealth concept in the translational research model.

PubMed

Silva, Angélica Baptista; Morel, Carlos Médicis; Moraes, Ilara Hämmerli Sozzi de

2014-04-01

To review the conceptual relationship between telehealth and translational research. Bibliographical search on telehealth was conducted in the Scopus, Cochrane BVS, LILACS and MEDLINE databases to find experiences of telehealth in conjunction with discussion of translational research in health. The search retrieved eight studies based on analysis of models of the five stages of translational research and the multiple strands of public health policy in the context of telehealth in Brazil. The models were applied to telehealth activities concerning the Network of Human Milk Banks, in the Telemedicine University Network. The translational research cycle of human milk collected, stored and distributed presents several integrated telehealth initiatives, such as video conferencing, and software and portals for synthesizing knowledge, composing elements of an information ecosystem, mediated by information and communication technologies in the health system. Telehealth should be composed of a set of activities in a computer mediated network promoting the translation of knowledge between research and health services.

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Massive problem reports mining and analysis based parallelism for similar search

NASA Astrophysics Data System (ADS)

Zhou, Ya; Hu, Cailin; Xiong, Han; Wei, Xiafei; Li, Ling

2017-05-01

Massive problem reports and solutions accumulated over time and continuously collected in XML Spreadsheet (XMLSS) format from enterprises and organizations, which record a series of comprehensive description about problems that can help technicians to trace problems and their solutions. It's a significant and challenging issue to effectively manage and analyze these massive semi-structured data to provide similar problem solutions, decisions of immediate problem and assisting product optimization for users during hardware and software maintenance. For this purpose, we build a data management system to manage, mine and analyze these data search results that can be categorized and organized into several categories for users to quickly find out where their interesting results locate. Experiment results demonstrate that this system is better than traditional centralized management system on the performance and the adaptive capability of heterogeneous data greatly. Besides, because of re-extracting topics, it enables each cluster to be described more precise and reasonable.

ExoDat Information System at CeSAM

NASA Astrophysics Data System (ADS)

Agneray, F.; Moreau, C.; Chabaud, P.; Damiani, C.; Deleuil, M.

2014-05-01

CoRoT (Convection Rotation and planetary transits) is a space based mission led by French space agency (CNES) in association with French and international laboratories. One of CoRoT's goal is to detect exoplanets by the transit method. The Exoplanet Database (Exodat) is a VO compliant information system for the CoRoT exoplanet program. The main functions of ExoDat are to provide a source catalog for the observation fields and targets selection; to characterize the CoRoT targets (spectral type, variability , contamination...);and to support follow up programs. ExoDat is built using the AstroNomical Information System (ANIS) developed by the CeSAM (Centre de donneeS Astrophysique de Marseille). It offers download of observation catalogs and additional services like: search, extract and display data by using a combination of criteria, object list, and cone-search interfaces. Web services have been developed to provide easy access for user's softwares and pipelines.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.

PubMed

de Andrade, Roberto R S; Vaslin, Maite F S

2014-03-07

Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

PubMed Central

2014-01-01

Background Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. Methods In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. Results The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. Conclusions SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. Availability and implementation SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/. PMID:24607237

Formal specification and verification of Ada software

NASA Technical Reports Server (NTRS)

Hird, Geoffrey R.

1991-01-01

The use of formal methods in software development achieves levels of quality assurance unobtainable by other means. The Larch approach to specification is described, and the specification of avionics software designed to implement the logic of a flight control system is given as an example. Penelope is described which is an Ada-verification environment. The Penelope user inputs mathematical definitions, Larch-style specifications and Ada code and performs machine-assisted proofs that the code obeys its specifications. As an example, the verification of a binary search function is considered. Emphasis is given to techniques assisting the reuse of a verification effort on modified code.

Automated Big Data Analysis in Bottom-up and Targeted Proteomics

PubMed Central

van der Plas-Duivesteijn, Suzanne; Domański, Dominik; Smith, Derek; Borchers, Christoph; Palmblad, Magnus; Mohamme, Yassene

2014-01-01

Similar to other data intensive sciences, analyzing mass spectrometry-based proteomics data involves multiple steps and diverse software using different algorithms and data formats and sizes. Besides that the distributed and evolving nature of the data in online repositories, another challenge is that a scientists have to deal with many steps of analysis pipelines. A documented data processing is also becoming an essential part for the overall reproducibility of the results. Thanks to different e-Science initiatives, scientific workflow engines have become a means for automated, sharable and reproducible data processing. While these are designed as general tools, they can be employed to solve different challenges that we are facing in handling our Big Data. Here we present three use cases: improving the performance of different spectral search engines by decomposing input data and recomposing the resulting files, building spectral libraries from more than 20 million spectra, and integrating information from multiple resources to select most appropriate peptides for targeted proteomics analyses. The three use cases demonstrate different challenges in exploiting proteomics data analysis. In the first we integrate local and cloud processing resources in order to obtain better performance resulting in more than 30-fold speed improvement. By considering search engines as legacy software our solution is applicable to multiple search algorithms. The second use case is an example of automated processing of many data files of different sizes and locations, starting with raw data and ending with the final, ready-to-use library. This demonstrates the robustness and fault tolerance when dealing with huge amount data stored in multiple files. The third use case demonstrates retrieval and integration of information and data from multiple online repositories. In addition to the diversity of data formats and Web interfaces, this use case also illustrates how to deal with incomplete data.

CINTEX: International Interoperability Extensions to EOSDIS

NASA Technical Reports Server (NTRS)

Graves, Sara J.

1997-01-01

A large part of the research under this cooperative agreement involved working with representatives of the DLR, NASDA, EDC, and NOAA-SAA data centers to propose a set of enhancements and additions to the EOSDIS Version 0 Information Management System (V0 IMS) Client/Server Message Protocol. Helen Conover of ITSL led this effort to provide for an additional geographic search specification (WRS Path/Row), data set- and data center-specific search criteria, search by granule ID, specification of data granule subsetting requests, data set-based ordering, and the addition of URLs to result messages. The V0 IMS Server Cookbook is an evolving document, providing resources and information to data centers setting up a VO IMS Server. Under this Cooperative Agreement, Helen Conover revised, reorganized, and expanded this document, and converted it to HTML. Ms. Conover has also worked extensively with the IRE RAS data center, CPSSI, in Russia. She served as the primary IMS contact for IRE-CPSSI and as IRE-CPSSI's liaison to other members of IMS and Web Gateway (WG) development teams. Her documentation of IMS problems in the IRE environment (Sun servers and low network bandwidth) led to a general restructuring of the V0 IMS Client message polling system. to the benefit of all IMS participants. In addition to the IMS server software and documentation. which are generally available to CINTEX sites, Ms. Conover also provided database design documentation and consulting, order tracking software, and hands-on testing and debug assistance to IRE. In the final pre-operational phase of IRE-CPSSI development, she also supplied information on configuration management, including ideas and processes in place at the Global Hydrology Resource Center (GHRC), an EOSDIS data center operated by ITSL.

Software architecture of the III/FBI segment of the FBI's integrated automated identification system

NASA Astrophysics Data System (ADS)

Booker, Brian T.

1997-02-01

This paper will describe the software architecture of the Interstate Identification Index (III/FBI) Segment of the FBI's Integrated Automated Fingerprint Identification System (IAFIS). IAFIS is currently under development, with deployment to begin in 1998. III/FBI will provide the repository of criminal history and photographs for criminal subjects, as well as identification data for military and civilian federal employees. Services provided by III/FBI include maintenance of the criminal and civil data, subject search of the criminal and civil data, and response generation services for IAFIS. III/FBI software will be comprised of both COTS and an estimated 250,000 lines of developed C code. This paper will describe the following: (1) the high-level requirements of the III/FBI software; (2) the decomposition of the III/FBI software into Computer Software Configuration Items (CSCIs); (3) the top-level design of the III/FBI CSCIs; and (4) the relationships among the developed CSCIs and the COTS products that will comprise the III/FBI software.

Characterizing internet health information seeking strategies by socioeconomic status: a mixed methods approach.

PubMed

Perez, Susan L; Kravitz, Richard L; Bell, Robert A; Chan, Man Shan; Paterniti, Debora A

2016-08-09

The Internet is valuable for those with limited access to health care services because of its low cost and wealth of information. Our objectives were to investigate how the Internet is used to obtain health-related information and how individuals with differing socioeconomic resources navigate it when presented with a health decision. Study participants were recruited from public settings and social service agencies. Participants listened to one of two clinical scenarios - consistent with influenza or bacterial meningitis - and then conducted an Internet search. Screen-capture video software captured the Internet search. Participant Internet search strategies were analyzed and coded for pre- and post-Internet search guess at diagnosis and information seeking patterns. Individuals who did not have a college degree and were recruited from locations offering social services were categorized as "lower socioeconomic status" (SES); the remainder was categorized as "higher SES." Participants were 78 Internet health information seekers, ranging from 21-35 years of age, who experienced barriers to accessing health care services. Lower-SES individuals were more likely to use an intuitive, rather than deliberative, approach to Internet health information seeking. Lower- and higher-SES participants did not differ in the tendency to make diagnostic guesses based on Internet searches. Lower-SES participants were more likely than their higher-SES counterparts to narrow the scope of their search. Our findings suggest that individuals with different levels of socioeconomic status vary in the heuristics and search patterns they rely upon to direct their searches. The influence and use of credible information in the process of making a decision is associated with education and prior experiences with healthcare services. Those with limited resources may be disadvantaged when turning to the Internet to make a health decision.

The Perth Automated Supernova Search

NASA Astrophysics Data System (ADS)

Williams, A. J.

1997-12-01

An automated search for supernovae in late spiral galaxies has been established at Perth Observatory, Western Australia. This automated search uses three low-cost PC-clone computers, a liquid nitrogen cooled CCD camera built locally, and a 61-cm telescope automated for the search. The images are all analysed automatically in real-time by routines in Perth Vista, the image processing system ported to the PC architecture for the search system. The telescope control software written for the project, Teljoy, maintains open-loop position accuracy better than 30" of arc after hundreds of jumps over an entire night. Total capital cost to establish and run this supernova search over the seven years of development and operation was around US$30,000. To date, the system has discovered a total of 6 confirmed supernovae, made an independent detection of a seventh, and detected one unconfirmed event assumed to be a supernova. The various software and hardware components of the search system are described in detail, the analysis of the first three years of data is discussed, and results presented. We find a Type Ib/c rate of 0.43 +/- 0.43 SNu, and a Type IIP rate of 0.86 +/- 0.49 SNu, where SNu are 'supernova units', expressed in supernovae per 10^10 solar blue luminosity galaxy per century. These values are for a Hubble constant of 75 km/s per Mpc, and scale as (H0/75)^2. The small number of discoveries has left large statistical uncertainties, but our strategy of frequent observations has reduced systematic errors - altering detection threshold or peak supernova luminosity by +/- 0.5 mag changes estimated rates by only around 20%. Similarly, adoption of different light curve templates for Type Ia and Type IIP supernovae has a minimal effect on the final statistics (2% and 4% change, respectively).

Search without Boundaries Using Simple APIs

USGS Publications Warehouse

Tong, Qi

2009-01-01

The U.S. Geological Survey (USGS) Library, where the author serves as the digital services librarian, is increasingly challenged to make it easier for users to find information from many heterogeneous information sources. Information is scattered throughout different software applications (i.e., library catalog, federated search engine, link resolver, and vendor websites), and each specializes in one thing. How could the library integrate the functionalities of one application with another and provide a single point of entry for users to search across? To improve the user experience, the library launched an effort to integrate the federated search engine into the library's intranet website. The result is a simple search box that leverages the federated search engine's built-in application programming interfaces (APIs). In this article, the author describes how this project demonstrated the power of APIs and their potential to be used by other enterprise search portals inside or outside of the library.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PubMed Central

Latendresse, Mario; Paley, Suzanne M.; Krummenacker, Markus; Ong, Quang D.; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M.; Caspi, Ron

2016-01-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. PMID:26454094

Software for Managing Inventory of Flight Hardware

NASA Technical Reports Server (NTRS)

Salisbury, John; Savage, Scott; Thomas, Shirman

2003-01-01

The Flight Hardware Support Request System (FHSRS) is a computer program that relieves engineers at Marshall Space Flight Center (MSFC) of most of the non-engineering administrative burden of managing an inventory of flight hardware. The FHSRS can also be adapted to perform similar functions for other organizations. The FHSRS affords a combination of capabilities, including those formerly provided by three separate programs in purchasing, inventorying, and inspecting hardware. The FHSRS provides a Web-based interface with a server computer that supports a relational database of inventory; electronic routing of requests and approvals; and electronic documentation from initial request through implementation of quality criteria, acquisition, receipt, inspection, storage, and final issue of flight materials and components. The database lists both hardware acquired for current projects and residual hardware from previous projects. The increased visibility of residual flight components provided by the FHSRS has dramatically improved the re-utilization of materials in lieu of new procurements, resulting in a cost savings of over $1.7 million. The FHSRS includes subprograms for manipulating the data in the database, informing of the status of a request or an item of hardware, and searching the database on any physical or other technical characteristic of a component or material. The software structure forces normalization of the data to facilitate inquiries and searches for which users have entered mixed or inconsistent values.

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data.

PubMed

Ficarro, Scott B; Alexander, William M; Marto, Jarrod A

2017-08-01

Although not yet truly 'comprehensive', modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments.

SemantGeo: Powering Ecological and Environment Data Discovery and Search with Standards-Based Geospatial Reasoning

NASA Astrophysics Data System (ADS)

Seyed, P.; Ashby, B.; Khan, I.; Patton, E. W.; McGuinness, D. L.

2013-12-01

Recent efforts to create and leverage standards for geospatial data specification and inference include the GeoSPARQL standard, Geospatial OWL ontologies (e.g., GAZ, Geonames), and RDF triple stores that support GeoSPARQL (e.g., AllegroGraph, Parliament) that use RDF instance data for geospatial features of interest. However, there remains a gap on how best to fuse software engineering best practices and GeoSPARQL within semantic web applications to enable flexible search driven by geospatial reasoning. In this abstract we introduce the SemantGeo module for the SemantEco framework that helps fill this gap, enabling scientists find data using geospatial semantics and reasoning. SemantGeo provides multiple types of geospatial reasoning for SemantEco modules. The server side implementation uses the Parliament SPARQL Endpoint accessed via a Tomcat servlet. SemantGeo uses the Google Maps API for user-specified polygon construction and JsTree for providing containment and categorical hierarchies for search. SemantGeo uses GeoSPARQL for spatial reasoning alone and in concert with RDFS/OWL reasoning capabilities to determine, e.g., what geofeatures are within, partially overlap with, or within a certain distance from, a given polygon. We also leverage qualitative relationships defined by the Gazetteer ontology that are composites of spatial relationships as well as administrative designations or geophysical phenomena. We provide multiple mechanisms for exploring data, such as polygon (map-based) and named-feature (hierarchy-based) selection, that enable flexible search constraints using boolean combination of selections. JsTree-based hierarchical search facets present named features and include a 'part of' hierarchy (e.g., measurement-site-01, Lake George, Adirondack Region, NY State) and type hierarchies (e.g., nodes in the hierarchy for WaterBody, Park, MeasurementSite), depending on the ';axis of choice' option selected. Using GeoSPARQL and aforementioned ontology, these hierarchies are constrained based on polygon selection, where the corresponding polygons of the contained features are visually rendered to assist exploration. Once measurement sites are plotted based on initial search, subsequent searches using JsTree selections can extend the previous based on nearby waterbodies in some semantic relationship of interest. For example, ';tributary of' captures water bodies that flow into the current one, and extending the original search to include tributaries of the observed water body is useful to environmental scientists for isolating the source of characteristic levels, including pollutants. Ultimately any SemantEco module can leverage SemantGeo's underlying APIs, leveraged in a deployment of SemantEco that combines EPA and USGS water quality data, and one customized for searching data available from the Darrin Freshwater Institute. Future work will address generating RDF geometry data from shape files, aligning RDF data sources to better leverage qualitative and spatial relationships, and validating newly generated RDF data adhering to the GeoSPARQL standard.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

C-CAT: a computer software used to analyze and select Chinese characters and character components for psychological research.

PubMed

Lo, Ming; Hue, Chih-Wei

2008-11-01

The Character-Component Analysis Toolkit (C-CAT) software was designed to assist researchers in constructing experimental materials using traditional Chinese characters. The software package contains two sets of character stocks: one suitable for research using literate adults as subjects and one suitable for research using schoolchildren as subjects. The software can identify linguistic properties, such as the number of strokes contained, the character-component pronunciation regularity, and the arrangement of character components within a character. Moreover, it can compute a character's linguistic frequency, neighborhood size, and phonetic validity with respect to a user-selected character stock. It can also search the selected character stock for similar characters or for character components with user-specified linguistic properties.

Combining results of multiple search engines in proteomics.

PubMed

Shteynberg, David; Nesvizhskii, Alexey I; Moritz, Robert L; Deutsch, Eric W

2013-09-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques.

Combining Results of Multiple Search Engines in Proteomics*

PubMed Central

Shteynberg, David; Nesvizhskii, Alexey I.; Moritz, Robert L.; Deutsch, Eric W.

2013-01-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques. PMID:23720762

MedlinePlus Connect: Frequently Asked Questions (FAQs)

MedlinePlus

... topic data in XML format. Using the Web service, software developers can build applications that utilize MedlinePlus health topic information. The service accepts keyword searches as requests and returns relevant ...

Storage and retrieval of digital images in dermatology.

PubMed

Bittorf, A; Krejci-Papa, N C; Diepgen, T L

1995-11-01

Differential diagnosis in dermatology relies on the interpretation of visual information in the form of clinical and histopathological images. Up until now, reference images have had to be retrieved from textbooks and/or appropriate journals. To overcome inherent limitations of those storage media with respect to the number of images stored, display, and search parameters available, we designed a computer-based database of digitized dermatologic images. Images were taken from the photo archive of the Dermatological Clinic of the University of Erlangen. A database was designed using the Entity-Relationship approach. It was implemented on a PC-Windows platform using MS Access* and MS Visual Basic®. As WWW-server a Sparc 10 workstation was used with the CERN Hypertext-Transfer-Protocol-Daemon (httpd) 3.0 pre 6 software running. For compressed storage on a hard drive, a quality factor of 60 allowed on-screen differential diagnosis and corresponded to a compression factor of 1:35 for clinical images and 1:40 for histopathological images. Hierarchical keys of clinical or histopathological criteria permitted multi-criteria searches. A script using the Common Gateway Interface (CGI) enabled remote search and image retrieval via the World-Wide-Web (W3). A dermatologic image database, featurig clinical and histopathological images was constructed which allows for multi-parameter searches and world-wide remote access.

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

Mitchell, Dean J.; Harding, Lee T.

Isotope identification algorithms that are contained in the Gamma Detector Response and Analysis Software (GADRAS) can be used for real-time stationary measurement and search applications on platforms operating under Linux or Android operating sys-tems. Since the background radiation can vary considerably due to variations in natu-rally-occurring radioactive materials (NORM), spectral algorithms can be substantial-ly more sensitive to threat materials than search algorithms based strictly on count rate. Specific isotopes or interest can be designated for the search algorithm, which permits suppression of alarms for non-threatening sources, such as such as medical radionuclides. The same isotope identification algorithms that are usedmore » for search ap-plications can also be used to process static measurements. The isotope identification algorithms follow the same protocols as those used by the Windows version of GADRAS, so files that are created under the Windows interface can be copied direct-ly to processors on fielded sensors. The analysis algorithms contain provisions for gain adjustment and energy lineariza-tion, which enables direct processing of spectra as they are recorded by multichannel analyzers. Gain compensation is performed by utilizing photopeaks in background spectra. Incorporation of this energy calibration tasks into the analysis algorithm also eliminates one of the more difficult challenges associated with development of radia-tion detection equipment.« less

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

PubMed

Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, Karina; Tauch, Andreas

2007-04-30

CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.

Architecture of the local spatial data infrastructure for regional climate change research

NASA Astrophysics Data System (ADS)

Titov, Alexander; Gordov, Evgeny

2013-04-01

Georeferenced datasets (meteorological databases, modeling and reanalysis results, etc.) are actively used in modeling and analysis of climate change for various spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their size which might constitute up to tens terabytes for a single dataset studies in the area of climate and environmental change require a special software support based on SDI approach. A dedicated architecture of the local spatial data infrastructure aiming at regional climate change analysis using modern web mapping technologies is presented. Geoportal is a key element of any SDI, allowing searching of geoinformation resources (datasets and services) using metadata catalogs, producing geospatial data selections by their parameters (data access functionality) as well as managing services and applications of cartographical visualization. It should be noted that due to objective reasons such as big dataset volume, complexity of data models used, syntactic and semantic differences of various datasets, the development of environmental geodata access, processing and visualization services turns out to be quite a complex task. Those circumstances were taken into account while developing architecture of the local spatial data infrastructure as a universal framework providing geodata services. So that, the architecture presented includes: 1. Effective in terms of search, access, retrieval and subsequent statistical processing, model of storing big sets of regional georeferenced data, allowing in particular to store frequently used values (like monthly and annual climate change indices, etc.), thus providing different temporal views of the datasets 2. General architecture of the corresponding software components handling geospatial datasets within the storage model 3. Metadata catalog describing in detail using ISO 19115 and CF-convention standards datasets used in climate researches as a basic element of the spatial data infrastructure as well as its publication according to OGC CSW (Catalog Service Web) specification 4. Computational and mapping web services to work with geospatial datasets based on OWS (OGC Web Services) standards: WMS, WFS, WPS 5. Geoportal as a key element of thematic regional spatial data infrastructure providing also software framework for dedicated web applications development To realize web mapping services Geoserver software is used since it provides natural WPS implementation as a separate software module. To provide geospatial metadata services GeoNetwork Opensource (http://geonetwork-opensource.org) product is planned to be used for it supports ISO 19115/ISO 19119/ISO 19139 metadata standards as well as ISO CSW 2.0 profile for both client and server. To implement thematic applications based on geospatial web services within the framework of local SDI geoportal the following open source software have been selected: 1. OpenLayers JavaScript library, providing basic web mapping functionality for the thin client such as web browser 2. GeoExt/ExtJS JavaScript libraries for building client-side web applications working with geodata services. The web interface developed will be similar to the interface of such popular desktop GIS applications, as uDIG, QuantumGIS etc. The work is partially supported by RF Ministry of Education and Science grant 8345, SB RAS Program VIII.80.2.1 and IP 131.

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

PubMed Central

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J.; Ball, Catherine A.

2010-01-01

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact: rshankar@stanford.edu PMID:20733062

Accelerated Profile HMM Searches

PubMed Central

Eddy, Sean R.

2011-01-01

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

Estimating Software-Development Costs With Greater Accuracy

NASA Technical Reports Server (NTRS)

Baker, Dan; Hihn, Jairus; Lum, Karen

2008-01-01

COCOMOST is a computer program for use in estimating software development costs. The goal in the development of COCOMOST was to increase estimation accuracy in three ways: (1) develop a set of sensitivity software tools that return not only estimates of costs but also the estimation error; (2) using the sensitivity software tools, precisely define the quantities of data needed to adequately tune cost estimation models; and (3) build a repository of software-cost-estimation information that NASA managers can retrieve to improve the estimates of costs of developing software for their project. COCOMOST implements a methodology, called '2cee', in which a unique combination of well-known pre-existing data-mining and software-development- effort-estimation techniques are used to increase the accuracy of estimates. COCOMOST utilizes multiple models to analyze historical data pertaining to software-development projects and performs an exhaustive data-mining search over the space of model parameters to improve the performances of effort-estimation models. Thus, it is possible to both calibrate and generate estimates at the same time. COCOMOST is written in the C language for execution in the UNIX operating system.

Designing the safety of healthcare. Participation of ergonomics to the design of cooperative systems in radiotherapy.

PubMed

Munoz, Maria Isabel; Bouldi, Nadia; Barcellini, Flore; Nascimento, Adelaide

2012-01-01

This communication deals with the involvement of ergonomists in a research-action design process of a software platform in radiotherapy. The goal of the design project is to enhance patient safety by designing a workflow software that supports cooperation between professionals producing treatment in radiotherapy. The general framework of our approach is the ergonomics management of a design process, which is based in activity analysis and grounded in participatory design. Two fields are concerned by the present action: a design environment which is a participatory design process that involves software designers, caregivers as future users and ergonomists; and a reference real work setting in radiotherapy. Observations, semi-structured interviews and participatory workshops allow the characterization of activity in radiotherapy dealing with uses of cooperative tools, sources of variability and non-ruled strategies to manage the variability of the situations. This production of knowledge about work searches to enhance the articulation between technocentric and anthropocentric approaches, and helps in clarifying design requirements. An issue of this research-action is to develop a framework to define the parameters of the workflow tool, and the conditions of its deployment.

Strategic Orientation in the Globalization of Software Firms

NASA Astrophysics Data System (ADS)

Dedrick, Jason; Kraemer, Kenneth L.; Carmel, Erran; Dunkle, Debora

In the search for profits, software firms are globalizing their development activities. Some firms achieve greater profits by becoming more efficient, whereas others do so by reaching new markets; some do both. This paper creates an a priori typology of strategies based on the extent to which firms are focused on operational improvement or market access, have a dual focus or are unfocused. We find that firms with these strategies differ in degree of internationalization, organization of offshoring and performance outcomes related to offshoring. Market-oriented firms receive a greater proportion of their total revenue from sales outside the U.S., showing a greater international orientation. They keep more of their offshore development in-house via captive operations. They also are most likely to report increased non-U.S. sales as a result of offshoring. On the other hand, operations-oriented firms have lower levels of international sales, are more likely to go offshore via outsourced software development, and achieve greater costs savings and labor force flexibility as a result of offshoring. Operations-oriented firms also face more obstacles in offshoring, perhaps because of their reliance on outsourcing. Dual focus firms generally achieve some of the best of both strategies, whereas unfocused firms achieve lower cost benefits.

Process Approach for Modeling of Machine and Tractor Fleet Structure

NASA Astrophysics Data System (ADS)

Dokin, B. D.; Aletdinova, A. A.; Kravchenko, M. S.; Tsybina, Y. S.

2018-05-01

The existing software complexes on modelling of the machine and tractor fleet structure are mostly aimed at solving the task of optimization. However, the creators, choosing only one optimization criterion and incorporating it in their software, provide grounds on why it is the best without giving a decision maker the opportunity to choose it for their enterprise. To analyze “bottlenecks” of machine and tractor fleet modelling, the authors of this article created a process model, in which they included adjustment to the plan of using machinery based on searching through alternative technologies. As a result, the following recommendations for software complex development have been worked out: the introduction of a database of alternative technologies; the possibility for a user to change the timing of the operations even beyond the allowable limits and in that case the calculation of the incurred loss; the possibility to rule out the solution of an optimization task, and if there is a necessity in it - the possibility to choose an optimization criterion; introducing graphical display of an annual complex of works, which could be enough for the development and adjustment of a business strategy.

The CARMEN software as a service infrastructure.

PubMed

Weeks, Michael; Jessop, Mark; Fletcher, Martyn; Hodge, Victoria; Jackson, Tom; Austin, Jim

2013-01-28

The CARMEN platform allows neuroscientists to share data, metadata, services and workflows, and to execute these services and workflows remotely via a Web portal. This paper describes how we implemented a service-based infrastructure into the CARMEN Virtual Laboratory. A Software as a Service framework was developed to allow generic new and legacy code to be deployed as services on a heterogeneous execution framework. Users can submit analysis code typically written in Matlab, Python, C/C++ and R as non-interactive standalone command-line applications and wrap them as services in a form suitable for deployment on the platform. The CARMEN Service Builder tool enables neuroscientists to quickly wrap their analysis software for deployment to the CARMEN platform, as a service without knowledge of the service framework or the CARMEN system. A metadata schema describes each service in terms of both system and user requirements. The search functionality allows services to be quickly discovered from the many services available. Within the platform, services may be combined into more complicated analyses using the workflow tool. CARMEN and the service infrastructure are targeted towards the neuroscience community; however, it is a generic platform, and can be targeted towards any discipline.

The igmspec database of public spectra probing the intergalactic medium

NASA Astrophysics Data System (ADS)

Prochaska, J. X.

2017-04-01

We describe v02 of igmspec, a database of publicly available ultraviolet, optical, and near-infrared spectra that probe the intergalactic medium (IGM). This database, a child of the specdb repository in the specdb github organization, comprises 403 277 unique sources and 434 686 spectra obtained with the world's greatest observatories. All of these data are distributed in a single ≈ 25GB HDF5 file maintained at the University of California Observatories and the University of California, Santa Cruz. The specdb software package includes Python scripts and modules for searching the source catalog and spectral datasets, and software links to the linetools package for spectral analysis. The repository also includes software to generate private spectral datasets that are compliant with International Virtual Observatory Alliance (IVOA) protocols and a Python-based interface for IVOA Simple Spectral Access queries. Future versions of igmspec will ingest other sources (e.g. gamma-ray burst afterglows) and other surveys as they become publicly available. The overall goal is to include every spectrum that effectively probes the IGM. Future databases of specdb may include publicly available galaxy spectra (exgalspec) and published supernovae spectra (snspec). The community is encouraged to join the effort on github: https://github.com/specdb.

The disagreement between the ideal observer and human observers in hardware and software imaging system optimization: theoretical explanations and evidence

NASA Astrophysics Data System (ADS)

He, Xin

2017-03-01

The ideal observer is widely used in imaging system optimization. One practical question remains open: do the ideal and human observers have the same preference in system optimization and evaluation? Based on the ideal observer's mathematical properties proposed by Barrett et. al. and the empirical properties of human observers investigated by Myers et. al., I attempt to pursue the general rules regarding the applicability of the ideal observer in system optimization. Particularly, in software optimization, the ideal observer pursues data conservation while humans pursue data presentation or perception. In hardware optimization, the ideal observer pursues a system with the maximum total information, while humans pursue a system with the maximum selected (e.g., certain frequency bands) information. These different objectives may result in different system optimizations between human and the ideal observers. Thus, an ideal observer optimized system is not necessarily optimal for humans. I cite empirical evidence in search and detection tasks, in hardware and software evaluation, in X-ray CT, pinhole imaging, as well as emission computed tomography to corroborate the claims. (Disclaimer: the views expressed in this work do not necessarily represent those of the FDA)

Informed-Proteomics: open-source software package for top-down proteomics

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

Park, Jungkap; Piehowski, Paul D.; Wilkins, Christopher

Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent needmore » to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.« less

JBEI Registry

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

Ham, Timothy

2008-12-01

The JBEI Registry is a software to store and manage to a database of biological parts. It is intended to be used as a web service that is accessed via a web browser. It is also capable of running as a desktop program for a single user. The registry software stores, indexes, categories, and allows users to enter, search, retrieve, and contruct biological constructs in silico. It is also able to communicate with other Registries for data sharing and exchange.

Using Dissimilarity Metrics to Identify Interesting Designs

NASA Technical Reports Server (NTRS)

Feather, Martin; Kiper, James

2006-01-01

A computer program helps to blend the power of automated-search software, which is able to generate large numbers of design solutions, with the insight of expert designers, who are able to identify preferred designs but do not have time to examine all the solutions. From among the many automated solutions to a given design problem, the program selects a smaller number of solutions that are worthy of scrutiny by the experts in the sense that they are sufficiently dissimilar from each other. The program makes the selection in an interactive process that involves a sequence of data-mining steps interspersed with visual displays of results of these steps to the experts. At crucial points between steps, the experts provide directives to guide the process. The program uses heuristic search techniques to identify nearly optimal design solutions and uses dissimilarity metrics defined by the experts to characterize the degree to which solutions are interestingly different. The search, data-mining, and visualization features of the program were derived from previously developed risk-management software used to support a risk-centric design methodology

A search for stellar occultations by Uranus, Neptune, Pluto, and their satellites: 1990-1999

NASA Technical Reports Server (NTRS)

Mink, Douglas J.

1991-01-01

A search for occultations of stars by Uranus, Neptune, and Pluto between 1990 and 1999 was carried out by combining ephemeris information and star positions using very accurate occultation modeling software. Stars from both the Space Telescope Guide Catalog and photographic plates taken by Arnold Klemola at Lick Observatory were compared with planet positions from the JPL DE-130 ephemeris, with local modifications for Pluto and Charon. Some 666 possible occultations by the Uranian ring, 143 possible occultations by Neptune, and 40 possible occultations by Pluto and/or Charon were found among stars with visual magnitudes as faint as 16. Before the star positions could be obtained, the occultation prediction software was used to aid many observers in observing the occultation of 28 Sagitarii by Saturn in July 1989. As a test on other outer solar system objects, 17 possible occultations were found in a search of the Guide Star Catalog for occultations by 2060 Chiron, and interesting object between Saturn and Uranus which shows both cometary and asteroidal properties.

LBT Distributed Archive: Status and Features

NASA Astrophysics Data System (ADS)

Knapic, C.; Smareglia, R.; Thompson, D.; Grede, G.

2011-07-01

After the first release of the LBT Distributed Archive, this successful collaboration is continuing within the LBT corporation. The IA2 (Italian Center for Astronomical Archive) team had updated the LBT DA with new features in order to facilitate user data retrieval while abiding by VO standards. To facilitate the integration of data from any new instruments, we have migrated to a new database, developed new data distribution software, and enhanced features in the LBT User Interface. The DBMS engine has been changed to MySQL. Consequently, the data handling software now uses java thread technology to update and synchronize the main storage archives on Mt. Graham and in Tucson, as well as archives in Trieste and Heidelberg, with all metadata and proprietary data. The LBT UI has been updated with additional features allowing users to search by instrument and some of the more important characteristics of the images. Finally, instead of a simple cone search service over all LBT image data, new instrument specific SIAP and cone search services have been developed. They will be published in the IVOA framework later this fall.

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.