WorldWideScience

Sample records for video annotation software

  1. Using video-annotation software to identify interactions in group therapies for schizophrenia: assessing reliability and associations with outcomes.

    Science.gov (United States)

    Orfanos, Stavros; Akther, Syeda Ferhana; Abdul-Basit, Muhammad; McCabe, Rosemarie; Priebe, Stefan

    2017-02-10

    Research has shown that interactions in group therapies for people with schizophrenia are associated with a reduction in negative symptoms. However, it is unclear which specific interactions in groups are linked with these improvements. The aims of this exploratory study were to i) develop and test the reliability of using video-annotation software to measure interactions in group therapies in schizophrenia and ii) explore the relationship between interactions in group therapies for schizophrenia with clinically relevant changes in negative symptoms. Video-annotation software was used to annotate interactions from participants selected across nine video-recorded out-patient therapy groups (N = 81). Using the Individual Group Member Interpersonal Process Scale, interactions were coded from participants who demonstrated either a clinically significant improvement (N = 9) or no change (N = 8) in negative symptoms at the end of therapy. Interactions were measured from the first and last sessions of attendance (>25 h of therapy). Inter-rater reliability between two independent raters was measured. Binary logistic regression analysis was used to explore the association between the frequency of interactive behaviors and changes in negative symptoms, assessed using the Positive and Negative Syndrome Scale. Of the 1275 statements that were annotated using ELAN, 1191 (93%) had sufficient audio and visual quality to be coded using the Individual Group Member Interpersonal Process Scale. Rater-agreement was high across all interaction categories (>95% average agreement). A higher frequency of self-initiated statements measured in the first session was associated with improvements in negative symptoms. The frequency of questions and giving advice measured in the first session of attendance was associated with improvements in negative symptoms; although this was only a trend. Video-annotation software can be used to reliably identify interactive behaviors in groups

  2. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  3. Current and future trends in marine image annotation software

    Science.gov (United States)

    Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

    2016-12-01

    Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images

  4. Video annotations of Mexican nature in a collaborative environment

    Science.gov (United States)

    Oropesa Morales, Lester Arturo; Montoya Obeso, Abraham; Hernández García, Rosaura; Cocolán Almeda, Sara Ivonne; García Vázquez, Mireya Saraí; Benois-Pineau, Jenny; Zamudio Fuentes, Luis Miguel; Martinez Nuño, Jesús A.; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    Multimedia content production and storage in repositories are now an increasingly widespread practice. Indexing concepts for search in multimedia libraries are very useful for users of the repositories. However the search tools of content-based retrieval and automatic video tagging, still do not have great consistency. Regardless of how these systems are implemented, it is of vital importance to possess lots of videos that have concepts tagged with ground truth (training and testing sets). This paper describes a novel methodology to make complex annotations on video resources through ELAN software. The concepts are annotated and related to Mexican nature in a High Level Features (HLF) from development set of TRECVID 2014 in a collaborative environment. Based on this set, each nature concept observed is tagged on each video shot using concepts of the TRECVid 2014 dataset. We also propose new concepts, -like tropical settings, urban scenes, actions, events, weather, places for name a few. We also propose specific concepts that best describe video content of Mexican culture. We have been careful to get the database tagged with concepts of nature and ground truth. It is evident that a collaborative environment is more suitable for annotation of concepts related to ground truth and nature. As a result a Mexican nature database was built. It also is the basis for testing and training sets to automatically classify new multimedia content of Mexican nature.

  5. Web-based Video Annotation and its Applications

    Science.gov (United States)

    Yamamoto, Daisuke; Nagao, Katashi

    In this paper, we developed a Web-based video annotation system, named iVAS (intelligent Video Annotation Server). Audiences can associate any video content on the Internet with annotations. The system analyzes video content in order to acquire cut/shot information and color histograms. And it also automatically generates a Web page for editing annotations. Then, audiences can create annotation data by two methods. The first one helps the users to create text data such as person/object names, scene descriptions, and comments interactively. The second method facilitates the users associating any video fragments with their subjective impression by just clicking a mouse button. The generated annotation data are accumulated and managed by an XML database connected with iVAS. We also developed some application systems based on annotations such as video retrieval, video simplification, and video-content-based community support. One of the major advantages of our approach is easy integration of hand-coded and automatically-generated (such as color histograms and cut/shot information) annotations. Additionally, since our annotation system is open for public, we must consider some reliability or correctness of annotation data. We also developed an automatic evaluation method of annotation reliability using the users' feedback. In the future, these fundamental technologies will contribute to the formation of new communities centered around video content.

  6. CARMA: Software for Continuous Affect Rating and Media Annotation

    Directory of Open Access Journals (Sweden)

    Jeffrey M. Girard

    2014-07-01

    Full Text Available CARMA is a media annotation program that collects continuous ratings while displaying audio and video files. It is designed to be highly user-friendly and easily customizable. Based on Gottman and Levenson’s affect rating dial, CARMA enables researchers and study participants to provide moment-by-moment ratings of multimedia files using a computer mouse or keyboard. The rating scale can be configured on a number of parameters including the labels for its upper and lower bounds, its numerical range, and its visual representation. Annotations can be displayed alongside the multimedia file and saved for easy import into statistical analysis software. CARMA provides a tool for researchers in affective computing, human-computer interaction, and the social sciences who need to capture the unfolding of subjective experience and observable behavior over time.

  7. Creating video-annotated discussions: An asynchronous alternative

    Directory of Open Access Journals (Sweden)

    Craig D. Howard

    2010-01-01

    Full Text Available In this article the authors illustrate the design and development of a pedagogical intervention using video annotations in a pre-service teacher education courrse. An annotation platform was selected and video was shot to create a video backdrop on which asynchronous discussions would take place. The article addresses design considerations in the selection of video, the editing process, and the development of a tutorial to lead learners through their first experience with this form of discussion. Learner participation samples were collected, and an analysis of the design process concludes the article.

  8. Automatic annotation of lecture videos for multimedia driven pedagogical platforms

    Directory of Open Access Journals (Sweden)

    Ali Shariq Imran

    2016-12-01

    Full Text Available Today’s eLearning websites are heavily loaded with multimedia contents, which are often unstructured, unedited, unsynchronized, and lack inter-links among different multimedia components. Hyperlinking different media modality may provide a solution for quick navigation and easy retrieval of pedagogical content in media driven eLearning websites. In addition, finding meta-data information to describe and annotate media content in eLearning platforms is challenging, laborious, prone to errors, and time-consuming task. Thus annotations for multimedia especially of lecture videos became an important part of video learning objects. To address this issue, this paper proposes three major contributions namely, automated video annotation, the 3-Dimensional (3D tag clouds, and the hyper interactive presenter (HIP eLearning platform. Combining existing state-of-the-art SIFT together with tag cloud, a novel approach for automatic lecture video annotation for the HIP is proposed. New video annotations are implemented automatically providing the needed random access in lecture videos within the platform, and a 3D tag cloud is proposed as a new way of user interaction mechanism. A preliminary study of the usefulness of the system has been carried out, and the initial results suggest that 70% of the students opted for using HIP as their preferred eLearning platform at Gjøvik University College (GUC.

  9. A video annotation methodology for interactive video sequence generation

    NARCIS (Netherlands)

    C.A. Lindley; R.A. Earnshaw; J.A. Vince

    2001-01-01

    textabstractThe FRAMES project within the RDN CRC (Cooperative Research Centre for Research Data Networks) has developed an experimental environment for dynamic virtual video sequence synthesis from databases of video data. A major issue for the development of dynamic interactive video applications

  10. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  11. Generating Protocol Software from CPN Models Annotated with Pragmatics

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars M.; Kindler, Ekkart

    2013-01-01

    and verify protocol software, but limited work exists on using CPN models of protocols as a basis for automated code generation. The contribution of this paper is a method for generating protocol software from a class of CPN models annotated with code generation pragmatics. Our code generation method...

  12. Eval: A software package for analysis of genome annotations

    Directory of Open Access Journals (Sweden)

    Brent Michael R

    2003-10-01

    Full Text Available Abstract Summary Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another. Input is in the standard Gene Transfer Format (GTF. Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited files. Availability To obtain the module package with documentation, go to http://genes.cse.wustl.edu/ and follow links for Resources, then Software. Please contact brent@cse.wustl.edu

  13. Radiation Tolerant Software Defined Video Processor Project

    Data.gov (United States)

    National Aeronautics and Space Administration — MaXentric's is proposing a radiation tolerant Software Define Video Processor, codenamed SDVP, for the problem of advanced motion imaging in the space environment....

  14. Creating Math Videos: Comparing Platforms and Software

    Science.gov (United States)

    Abbasian, Reza O.; Sieben, John T.

    2016-01-01

    In this paper we present a short tutorial on creating mini-videos using two platforms--PCs and tablets such as iPads--and software packages that work with these devices. Specifically, we describe the step-by-step process of creating and editing videos using a Wacom Intuos pen-tablet plus Camtasia software on a PC platform and using the software…

  15. SVA: software for annotating and visualizing sequenced human genomes.

    Science.gov (United States)

    Ge, Dongliang; Ruzzo, Elizabeth K; Shianna, Kevin V; He, Min; Pelak, Kimberly; Heinzen, Erin L; Need, Anna C; Cirulli, Elizabeth T; Maia, Jessica M; Dickson, Samuel P; Zhu, Mingfu; Singh, Abanish; Allen, Andrew S; Goldstein, David B

    2011-07-15

    Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Freely available on the web at http://www.svaproject.org.

  16. Handbook and Annotated Software Bibliography. Microcomputers in ABE.

    Science.gov (United States)

    Holter, Mary Patricia; Johnson, Carmen

    This handbook and annotated bibliography presents discussions, ideas, and resources useful to adult basic education (ABE) program teachers and administrators in implementing educational microcomputing, and describes microcomputer software programs that have been used successfully in ABE. The first part of the book, the handbook, is organized in…

  17. Outcomes and Perceptions of Annotated Video Feedback Following Psychomotor Skill Laboratories

    Science.gov (United States)

    Truskowski, S.; VanderMolen, J.

    2017-01-01

    This study sought to explore the effectiveness of annotated video technology for providing feedback to occupational therapy students learning transfers, range of motion and manual muscle testing. Fifty-seven first-year occupational therapy students were split into two groups. One received annotated video feedback during a transfer lab and…

  18. Real-time Classification of Gorilla Video Segments in Affective Categories Using Crowd-Sourced Annotations

    NARCIS (Netherlands)

    Schavemaker, J.G.M.; Thomas, E.D.R.; Havekes, A.

    2014-01-01

    In this contribution we present a method to classify segments of gorilla videos1 in different affective categories. The classification method is trained by crowd sourcing affective annotation. The trained classification then uses video features (computed from the video segments) to classify a new

  19. DNannotator: annotation software tool kit for regional genomic sequences

    OpenAIRE

    Liu, Chunyu; Bonner, Tom I.; Nguyen, Tu; Lyons, Jennifer L.; Christian, Susan L.; Gershon, Elliot S.

    2003-01-01

    Sequence annotation is essential for genomics-based research. Investigators of a specific genomic region who have developed abundant local discoveries such as genes and genetic markers, or have collected annotations from multiple resources, can be overwhelmed by the difficulty in creating local annotation and the complexity of integrating all the annotations. Presenting such integrated data in a form suitable for data mining and high-throughput experimental design is even more daunting. DNann...

  20. Performance evaluation software moving object detection and tracking in videos

    CERN Document Server

    Karasulu, Bahadir

    2013-01-01

    Performance Evaluation Software: Moving Object Detection and Tracking in Videos introduces a software approach for the real-time evaluation and performance comparison of the methods specializing in moving object detection and/or tracking (D&T) in video processing. Digital video content analysis is an important item for multimedia content-based indexing (MCBI), content-based video retrieval (CBVR) and visual surveillance systems. There are some frequently-used generic algorithms for video object D&T in the literature, such as Background Subtraction (BS), Continuously Adaptive Mean-shift (CMS),

  1. A Flexible Object-of-Interest Annotation Framework for Online Video Portals

    Directory of Open Access Journals (Sweden)

    Robert Sorschag

    2012-02-01

    Full Text Available In this work, we address the use of object recognition techniques to annotate what is shown where in online video collections. These annotations are suitable to retrieve specific video scenes for object related text queries which is not possible with the manually generated metadata that is used by current portals. We are not the first to present object annotations that are generated with content-based analysis methods. However, the proposed framework possesses some outstanding features that offer good prospects for its application in real video portals. Firstly, it can be easily used as background module in any video environment. Secondly, it is not based on a fixed analysis chain but on an extensive recognition infrastructure that can be used with all kinds of visual features, matching and machine learning techniques. New recognition approaches can be integrated into this infrastructure with low development costs and a configuration of the used recognition approaches can be performed even on a running system. Thus, this framework might also benefit from future advances in computer vision. Thirdly, we present an automatic selection approach to support the use of different recognition strategies for different objects. Last but not least, visual analysis can be performed efficiently on distributed, multi-processor environments and a database schema is presented to store the resulting video annotations as well as the off-line generated low-level features in a compact form. We achieve promising results in an annotation case study and the instance search task of the TRECVID 2011 challenge.

  2. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.

    Science.gov (United States)

    Gremme, Gordon; Steinbiss, Sascha; Kurtz, Stefan

    2013-01-01

    Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface.

  3. AGeS: a software system for microbial genome sequence annotation.

    Directory of Open Access Journals (Sweden)

    Kamal Kumar

    Full Text Available BACKGROUND: The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. METHODOLOGY: The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA. The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions.

  4. AGeS: A Software System for Microbial Genome Sequence Annotation

    Science.gov (United States)

    Kumar, Kamal; Desai, Valmik; Cheng, Li; Khitrov, Maxim; Grover, Deepak; Satya, Ravi Vijaya; Yu, Chenggang; Zavaljevski, Nela; Reifman, Jaques

    2011-01-01

    Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. Methodology The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions. PMID:21408217

  5. Making Educational and Scholarly Videos with Screen Capture Software

    Directory of Open Access Journals (Sweden)

    Mark L. Burkey

    2015-11-01

    Full Text Available This resource describes several options for making educational videos using “screencasting”, or “screen capture” software.  The author (who has over 300 screencasted videos on YouTube and indexed on his website, www.burkeyacademy.com describes the software and hardware tools needed, including some open source and free-to-use tools.  Links to some “how to” videos are included, as well as some links to other example videos demonstrating novel professional uses for screencasting.

  6. Bridging the Gap: Enriching YouTube Videos with Jazz Music Annotations

    Directory of Open Access Journals (Sweden)

    Stefan Balke

    2018-02-01

    Full Text Available Web services allow permanent access to music from all over the world. Especially in the case of web services with user-supplied content, e.g., YouTube™, the available metadata is often incomplete or erroneous. On the other hand, a vast amount of high-quality and musically relevant metadata has been annotated in research areas such as Music Information Retrieval (MIR. Although they have great potential, these musical annotations are often inaccessible to users outside the academic world. With our contribution, we want to bridge this gap by enriching publicly available multimedia content with musical annotations available in research corpora, while maintaining easy access to the underlying data. Our web-based tools offer researchers and music lovers novel possibilities to interact with and navigate through the content. In this paper, we consider a research corpus called the Weimar Jazz Database (WJD as an illustrating example scenario. The WJD contains various annotations related to famous jazz solos. First, we establish a link between the WJD annotations and corresponding YouTube videos employing existing retrieval techniques. With these techniques, we were able to identify 988 corresponding YouTube videos for 329 solos out of 456 solos contained in the WJD. We then embed the retrieved videos in a recently developed web-based platform and enrich the videos with solo transcriptions that are part of the WJD. Furthermore, we integrate publicly available data resources from the Semantic Web in order to extend the presented information, for example, with a detailed discography or artists-related information. Our contribution illustrates the potential of modern web-based technologies for the digital humanities, and novel ways for improving access and interaction with digitized multimedia content.

  7. High-quality real-time temporal segmentation tool for video editing software

    OpenAIRE

    Cuevas Rodríguez, Carlos; García Santos, Narciso

    2012-01-01

    The increasing use of video editing software has resulted in a necessity for faster and more efficient editing tools. Here, we propose a lightweight high-quality video indexing tool that is suitable for video editing software.

  8. Collaborative web-based annotation of video footage of deep-sea life, ecosystems and geological processes

    Science.gov (United States)

    Kottmann, R.; Ratmeyer, V.; Pop Ristov, A.; Boetius, A.

    2012-04-01

    More and more seagoing scientific expeditions use video-controlled research platforms such as Remote Operating Vehicles (ROV), Autonomous Underwater Vehicles (AUV), and towed camera systems. These produce many hours of video material which contains detailed and scientifically highly valuable footage of the biological, chemical, geological, and physical aspects of the oceans. Many of the videos contain unique observations of unknown life-forms which are rare, and which cannot be sampled and studied otherwise. To make such video material online accessible and to create a collaborative annotation environment the "Video Annotation and processing platform" (V-App) was developed. A first solely web-based installation for ROV videos is setup at the German Center for Marine Environmental Sciences (available at http://videolib.marum.de). It allows users to search and watch videos with a standard web browser based on the HTML5 standard. Moreover, V-App implements social web technologies allowing a distributed world-wide scientific community to collaboratively annotate videos anywhere at any time. It has several features fully implemented among which are: • User login system for fine grained permission and access control • Video watching • Video search using keywords, geographic position, depth and time range and any combination thereof • Video annotation organised in themes (tracks) such as biology and geology among others in standard or full screen mode • Annotation keyword management: Administrative users can add, delete, and update single keywords for annotation or upload sets of keywords from Excel-sheets • Download of products for scientific use This unique web application system helps making costly ROV videos online available (estimated cost range between 5.000 - 10.000 Euros per hour depending on the combination of ship and ROV). Moreover, with this system each expert annotation adds instantaneous available and valuable knowledge to otherwise uncharted

  9. 76 FR 45859 - In the Matter of Certain Video Analytics Software, Systems, Components Thereof, and Products...

    Science.gov (United States)

    2011-08-01

    ... COMMISSION In the Matter of Certain Video Analytics Software, Systems, Components Thereof, and Products... analytics software, systems, components thereof, and products containing same by reason of infringement of... after importation of certain video analytics software, systems, components thereof, and products...

  10. 77 FR 45376 - Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same...

    Science.gov (United States)

    2012-07-31

    ... COMMISSION Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same... analytics software, systems, components thereof, and products containing same by reason of infringement of... after importation of certain video analytics software, systems, components thereof, and products...

  11. 77 FR 39509 - Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same...

    Science.gov (United States)

    2012-07-03

    ... COMMISSION Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same... Trade Commission has received a complaint entitled Certain Video Analytics Software, Systems, Components... analytics software, systems, components thereof, and products containing same. The complaint names as...

  12. Annotated Bibliography on Human Factors in Software Development

    Science.gov (United States)

    1979-06-01

    CTECHIUCAL REPORT NO. MTR-2874). BEDFORD, MASSACHUSETTS: MITRE CORP., 1975. 24 SOFTWARE ENGINEERING BEMER . R.W. A SOFTWARE ENGINEERIS WORKSHOP: TOOLS AND...B.So BARTOL, K.M. 19 BAYER, R. 2D, 54, 173 PEARD, I’M.H ° 16, 17, 21 BECKER, C.A. 96, 153, 266 BECKMAN, A. 22 BELL, D.E. 23 BEMER , k°V. 24 BERGER, R.Mo

  13. What do we do with all this video? Better understanding public engagement for image and video annotation

    Science.gov (United States)

    Wiener, C.; Miller, A.; Zykov, V.

    2016-12-01

    Advanced robotic vehicles are increasingly being used by oceanographic research vessels to enable more efficient and widespread exploration of the ocean, particularly the deep ocean. With cutting-edge capabilities mounted onto robotic vehicles, data at high resolutions is being generated more than ever before, enabling enhanced data collection and the potential for broader participation. For example, high resolution camera technology not only improves visualization of the ocean environment, but also expands the capacity to engage participants remotely through increased use of telepresence and virtual reality techniques. Schmidt Ocean Institute is a private, non-profit operating foundation established to advance the understanding of the world's oceans through technological advancement, intelligent observation and analysis, and open sharing of information. Telepresence-enabled research is an important component of Schmidt Ocean Institute's science research cruises, which this presentation will highlight. Schmidt Ocean Institute is one of the only research programs that make their entire underwater vehicle dive series available online, creating a collection of video that enables anyone to follow deep sea research in real time. We encourage students, educators and the general public to take advantage of freely available dive videos. Additionally, other SOI-supported internet platforms, have engaged the public in image and video annotation activities. Examples of these new online platforms, which utilize citizen scientists to annotate scientific image and video data will be provided. This presentation will include an introduction to SOI-supported video and image tagging citizen science projects, real-time robot tracking, live ship-to-shore communications, and an array of outreach activities that enable scientists to interact with the public and explore the ocean in fascinating detail.

  14. Software Suite for Gene and Protein Annotation Prediction and Similarity Search.

    Science.gov (United States)

    Chicco, Davide; Masseroli, Marco

    2015-01-01

    In the computational biology community, machine learning algorithms are key instruments for many applications, including the prediction of gene-functions based upon the available biomolecular annotations. Additionally, they may also be employed to compute similarity between genes or proteins. Here, we describe and discuss a software suite we developed to implement and make publicly available some of such prediction methods and a computational technique based upon Latent Semantic Indexing (LSI), which leverages both inferred and available annotations to search for semantically similar genes. The suite consists of three components. BioAnnotationPredictor is a computational software module to predict new gene-functions based upon Singular Value Decomposition of available annotations. SimilBio is a Web module that leverages annotations available or predicted by BioAnnotationPredictor to discover similarities between genes via LSI. The suite includes also SemSim, a new Web service built upon these modules to allow accessing them programmatically. We integrated SemSim in the Bio Search Computing framework (http://www.bioinformatics.deib. polimi.it/bio-seco/seco/), where users can exploit the Search Computing technology to run multi-topic complex queries on multiple integrated Web services. Accordingly, researchers may obtain ranked answers involving the computation of the functional similarity between genes in support of biomedical knowledge discovery.

  15. Developing and Testing a Video Tutorial for Software Training

    NARCIS (Netherlands)

    van der Meij, Hans

    2014-01-01

    Purpose: Video tutorials for software training are rapidly becoming popular. A set of dedicated guidelines for the construction of such tutorials was recently advanced in Technical Communication (Van der Meij & Van der Meij, 2013). The present study set out to assess the cognitive and motivational

  16. Pragmatics annotated coloured petri nets for protocol software generation and verification

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge Fagerland; Kristensen, Lars M.; Kindler, Ekkart

    2016-01-01

    Pragmatics Annotated Coloured Petri Nets (PA-CPNs) are a restricted class of Coloured Petri Nets (CPNs) developed to support automated generation of protocol software. The practical application of PA-CPNs and the supporting PetriCode software tool have been discussed and evaluated in earlier pape...... already. The contribution of this paper is to give a formal definition of PA-CPNs, motivate the definitions, and demonstrate how the structure of PA-CPNs can be exploited for more efficient verification....

  17. Pragmatics Annotated Coloured Petri Nets for Protocol Software Generation and Verification

    DEFF Research Database (Denmark)

    Fagerland Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    2015-01-01

    PetriCode is a tool that supports automated generation of protocol software from a restricted class of Coloured Petri Nets (CPNs) called Pragmatics Annotated Coloured Petri Nets (PA-CPNs). Petri-Code and PA-CPNs have been designed with five main requirements in mind, which include the same model...

  18. DARMA: Software for dual axis rating and media annotation.

    Science.gov (United States)

    Girard, Jeffrey M; C Wright, Aidan G

    2017-06-20

    Continuous measurement systems provide a means of measuring dynamic behavioral and experiential processes as they play out over time. DARMA is a modernized continuous measurement system that synchronizes media playback and the continuous recording of two-dimensional measurements. These measurements can be observational or self-reported and are provided in real-time through the manipulation of a computer joystick. DARMA also provides tools for reviewing and comparing collected measurements and for customizing various settings. DARMA is a domain-independent software tool that was designed to aid researchers who are interested in gaining a deeper understanding of behavior and experience. It is especially well-suited to the study of affective and interpersonal processes, such as the perception and expression of emotional states and the communication of social signals. DARMA is open-source using the GNU General Public License (GPL) and is available for free download from http://darma.jmgirard.com .

  19. Pragmatics Annotated Coloured Petri Nets for Protocol Software Generation and Verification

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    This paper presents the formal definition of Pragmatics Annotated Coloured Petri Nets (PA-CPNs). PA-CPNs represent a class of Coloured Petri Nets (CPNs) that are designed to support automated code genera-tion of protocol software. PA-CPNs restrict the structure of CPN models and allow Petri net...... elements to be annotated with so-called pragmatics, which are exploited for code generation. The approach and tool for gen-erating code is called PetriCode and has been discussed and evaluated in earlier work already. The contribution of this paper is to give a formal def-inition for PA-CPNs; in addition...

  20. 77 FR 75659 - Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same...

    Science.gov (United States)

    2012-12-21

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same... the United States after importation of certain video analytics software systems, components thereof...

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

    Directory of Open Access Journals (Sweden)

    Peterson Elena S

    2012-04-01

    Full Text Available Abstract 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

  2. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

    Science.gov (United States)

    Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul

    2017-01-01

    The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). http://www.ensembl.org.

  3. Unsupervised decoding of long-term, naturalistic human neural recordings with automated video and audio annotations

    Directory of Open Access Journals (Sweden)

    Nancy X.R. Wang

    2016-04-01

    Full Text Available Fully automated decoding of human activities and intentions from direct neural recordings is a tantalizing challenge in brain-computer interfacing. Implementing Brain Computer Interfaces (BCIs outside carefully controlled experiments in laboratory settings requires adaptive and scalable strategies with minimal supervision. Here we describe an unsupervised approach to decoding neural states from naturalistic human brain recordings. We analyzed continuous, long-term electrocorticography (ECoG data recorded over many days from the brain of subjects in a hospital room, with simultaneous audio and video recordings. We discovered coherent clusters in high-dimensional ECoG recordings using hierarchical clustering and automatically annotated them using speech and movement labels extracted from audio and video. To our knowledge, this represents the first time techniques from computer vision and speech processing have been used for natural ECoG decoding. Interpretable behaviors were decoded from ECoG data, including moving, speaking and resting; the results were assessed by comparison with manual annotation. Discovered clusters were projected back onto the brain revealing features consistent with known functional areas, opening the door to automated functional brain mapping in natural settings.

  4. AGeS: A Software System for Microbial Genome Sequence Annotation

    Science.gov (United States)

    2011-03-01

    management system ( RDBMS ) to provide persistence support for workflow and sequence annotation data. AGeS also supports the use of external RDBMS , such as...Chenggang Yu, Nela Zavaljevski, Jaques Reifman* DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and...bioinformatics tools and databases, many of which are parallelized for high-throughput performance . Methodology: The AGeS system supports three main

  5. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

    Directory of Open Access Journals (Sweden)

    Pontarotti Pierre

    2005-08-01

    Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

  6. Big Davids – Real-Time Sensor Classification. Real-time classification of gorilla video segments in affective categories using crowd-sourced annotations

    NARCIS (Netherlands)

    Havekes, A.; Thomas, E.D.R.; Schavemaker, J.G.M.

    2013-01-01

    In this sheet book we present a method to classify segments of gorilla videos in different affective categories. The classification method is trained by crowd sourcing annotation. The trained classification than uses video features (computed from the video segments) to classify a new video segment

  7. Video Games and Software Engineers : Designing a study based on the benefits from Video Games and how they can improve Software Engineers

    OpenAIRE

    Cosic Prica, Srdjan

    2017-01-01

    Context: This is a study about investigating if playing video games can improve any skills and characteristics in a software engineer. Due to lack of resources and time, this study will focus on designing a study that others may use to measure the results and if video games actually can improve software engineers. Objectives: The main objectives are finding the benefits of playing video games and how those benefits are discovered. Meaning what types of games and for how long someone needs to ...

  8. Automated annotation and quantitative description of ultrasound videos of the fetal heart.

    Science.gov (United States)

    Bridge, Christopher P; Ioannou, Christos; Noble, J Alison

    2017-02-01

    Interpretation of ultrasound videos of the fetal heart is crucial for the antenatal diagnosis of congenital heart disease (CHD). We believe that automated image analysis techniques could make an important contribution towards improving CHD detection rates. However, to our knowledge, no previous work has been done in this area. With this goal in mind, this paper presents a framework for tracking the key variables that describe the content of each frame of freehand 2D ultrasound scanning videos of the healthy fetal heart. This represents an important first step towards developing tools that can assist with CHD detection in abnormal cases. We argue that it is natural to approach this as a sequential Bayesian filtering problem, due to the strong prior model we have of the underlying anatomy, and the ambiguity of the appearance of structures in ultrasound images. We train classification and regression forests to predict the visibility, location and orientation of the fetal heart in the image, and the viewing plane label from each frame. We also develop a novel adaptation of regression forests for circular variables to deal with the prediction of cardiac phase. Using a particle-filtering-based method to combine predictions from multiple video frames, we demonstrate how to filter this information to give a temporally consistent output at real-time speeds. We present results on a challenging dataset gathered in a real-world clinical setting and compare to expert annotations, achieving similar levels of accuracy to the levels of inter- and intra-observer variation. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  9. 77 FR 75188 - Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same...

    Science.gov (United States)

    2012-12-19

    ... COMMISSION Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same... certain video analytics software, systems, components thereof, and products containing same by reason of..., Inc. The remaining respondents are Bosch Security Systems, Inc.; Robert Bosch GmbH; Bosch...

  10. 77 FR 808 - Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same...

    Science.gov (United States)

    2012-01-06

    ... COMMISSION Certain Video Analytics Software, Systems, Components Thereof, and Products Containing Same... States after importation of certain video analytics software, systems, components thereof, and products...; Bosch Security Systems, Inc. of Fairpoint, New York; Samsung Techwin Co., Ltd. of Seoul, Korea; Samsung...

  11. Eight guidelines for the design of instructional videos for software training

    NARCIS (Netherlands)

    van der Meij, Hans; van der Meij, Jan

    2013-01-01

    Purpose: Video has become a popular means for delivering "how to" information about a wide variety of software tasks. With video rapidly becoming a major instructional method, the question arises of their effectiveness for software training. This paper provides a set of eight guidelines for the

  12. STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post-Translational Modifications.

    Science.gov (United States)

    Spencer, Jean L; Bhatia, Vivek N; Whelan, Stephen A; Costello, Catherine E; McComb, Mark E

    2013-12-01

    The identification of protein post-translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for performing fast and easy characterization of global PTM changes and differential comparison of PTMs across groups of data obtained from liquid chromatography-tandem mass spectrometry experiments. STRAP PTM (Software Tool for Rapid Annotation of Proteins: Post-Translational Modification edition) is a program that was developed to facilitate the characterization of PTMs using spectral counting and a novel scoring algorithm to accelerate the identification of differential PTMs from complex data sets. The software facilitates multi-sample comparison by collating, scoring, and ranking PTMs and by summarizing data visually. The freely available software (beta release) installs on a PC and processes data in protXML format obtained from files parsed through the Trans-Proteomic Pipeline. The easy-to-use interface allows examination of results at protein, peptide, and PTM levels, and the overall design offers tremendous flexibility that provides proteomics insight beyond simple assignment and counting.

  13. Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

    Directory of Open Access Journals (Sweden)

    Dunning Alison M

    2009-06-01

    Full Text Available Abstract Background In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once. Implementation We created Seq4SNPs, a web-based, walk-away software that can process one to several hundred SNPs given rs numbers as input. It outputs a file of fully annotated sequences formatted for one of three proprietary design softwares: TaqMan's Primer-By-Design FileBuilder, Sequenom's iPLEX or SNPstream's Autoprimer, as well as unannotated fasta sequences. We found genotyping assays to be inhibited by repetitive sequences or the presence of additional variations flanking the SNP under test, and in multiplexes, repetitive sequence flanking one SNP adversely affects multiple assays. Assay design software programs avoid such regions if the input sequences are appropriately annotated, so we used Seq4SNPs to provide suitably annotated input sequences, and improved our genotyping success rate. Adjacent SNPs can also be avoided, by annotating sequences used as input for primer design. Conclusion The accuracy of annotation by Seq4SNPs is significantly better than manual annotation (P Using Seq4SNPs to incorporate all annotation for additional SNPs and repetitive elements into sequences, for genotyping assay designer software, minimizes assay failure at the design stage, reducing the cost of genotyping. Seq4SNPs provides a rapid route for replacement of poor test SNP sequences. We routinely use this software for assay sequence preparation. Seq4SNPs is available as a service at http://moya.srl.cam.ac.uk/oncology/bio/s4shome.html and http://moya.srl

  14. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

    Science.gov (United States)

    Zhang, Jia; Yang, Ming-Kun; Zeng, Honghui; Ge, Feng

    2016-11-01

    Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Development of a Kinect Software Tool to Classify Movements during Active Video Gaming

    National Research Council Canada - National Science Library

    Rosenberg, Michael; Thornton, Ashleigh L; Lay, Brendan S; Ward, Brodie; Nathan, David; Hunt, Daniel; Braham, Rebecca

    2016-01-01

    ... movement during active video game play in relationship to fundamental movement skills. The aim of this study was to validate software utilising Kinect sensor motion capture technology to recognise fundamental movement skills (FMS...

  16. The Use of Video Technology for the Fast-Prototyping of Artificially Intelligent Software.

    Science.gov (United States)

    Klein, Gary L.

    This paper describes the use of video to provide a screenplay depiction of a proposed artificial intelligence software system. Advantages of such use are identified: (1) the video can be used to provide a clear conceptualization of the proposed system; (2) it can illustrate abstract technical concepts; (3) it can simulate the functions of the…

  17. Data Reduction and Control Software for Meteor Observing Stations Based on CCD Video Systems

    Science.gov (United States)

    Madiedo, J. M.; Trigo-Rodriguez, J. M.; Lyytinen, E.

    2011-01-01

    The SPanish Meteor Network (SPMN) is performing a continuous monitoring of meteor activity over Spain and neighbouring countries. The huge amount of data obtained by the 25 video observing stations that this network is currently operating made it necessary to develop new software packages to accomplish some tasks, such as data reduction and remote operation of autonomous systems based on high-sensitivity CCD video devices. The main characteristics of this software are described here.

  18. Self-evaluation and peer-feedback of medical students' communication skills using a web-based video annotation system. Exploring content and specificity.

    Science.gov (United States)

    Hulsman, Robert L; van der Vloodt, Jane

    2015-03-01

    Self-evaluation and peer-feedback are important strategies within the reflective practice paradigm for the development and maintenance of professional competencies like medical communication. Characteristics of the self-evaluation and peer-feedback annotations of medical students' video recorded communication skills were analyzed. Twenty-five year 4 medical students recorded history-taking consultations with a simulated patient, uploaded the video to a web-based platform, marked and annotated positive and negative events. Peers reviewed the video and self-evaluations and provided feedback. Analyzed were the number of marked positive and negative annotations and the amount of text entered. Topics and specificity of the annotations were coded and analyzed qualitatively. Students annotated on average more negative than positive events. Additional peer-feedback was more often positive. Topics most often related to structuring the consultation. Students were most critical about their biomedical topics. Negative annotations were more specific than positive annotations. Self-evaluations were more specific than peer-feedback and both show a significant correlation. Four response patterns were detected that negatively bias specificity assessment ratings. Teaching students to be more specific in their self-evaluations may be effective for receiving more specific peer-feedback. Videofragmentrating is a convenient tool to implement reflective practice activities like self-evaluation and peer-feedback to the classroom in the teaching of clinical skills. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  19. Rapid prototyping of an automated video surveillance system: a hardware-software co-design approach

    Science.gov (United States)

    Ngo, Hau T.; Rakvic, Ryan N.; Broussard, Randy P.; Ives, Robert W.

    2011-06-01

    FPGA devices with embedded DSP and memory blocks, and high-speed interfaces are ideal for real-time video processing applications. In this work, a hardware-software co-design approach is proposed to effectively utilize FPGA features for a prototype of an automated video surveillance system. Time-critical steps of the video surveillance algorithm are designed and implemented in the FPGAs logic elements to maximize parallel processing. Other non timecritical tasks are achieved by executing a high level language program on an embedded Nios-II processor. Pre-tested and verified video and interface functions from a standard video framework are utilized to significantly reduce development and verification time. Custom and parallel processing modules are integrated into the video processing chain by Altera's Avalon Streaming video protocol. Other data control interfaces are achieved by connecting hardware controllers to a Nios-II processor using Altera's Avalon Memory Mapped protocol.

  20. GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes.

    Science.gov (United States)

    Altermann, Eric; Lu, Jingli; McCulloch, Alan

    2017-01-01

    Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.

  1. Automatic Annotation of Formula 1 Races for Content-Based Video Retrieval

    NARCIS (Netherlands)

    Mihajlovic, V.; Petkovic, M.

    2001-01-01

    Content-based video retrieval is emerging as an important part in the process of utilization of various multimedia documents. In this report we present a novel system for the automatic indexing and content-based retrieval of multimedia documents. We chose the domain of Formula 1 sport videos because

  2. Simulation and video software development for soil consolidation testing

    NARCIS (Netherlands)

    Karim, Usama F.A.

    2003-01-01

    The development techniques and file structures of CTM, a novel multi-media (computer simulation and video) package on consolidation and laboratory consolidation testing, are presented in this paper. A courseware tool called Authorware proved to be versatile for building the package and the paper

  3. In-network adaptation of SHVC video in software-defined networks

    Science.gov (United States)

    Awobuluyi, Olatunde; Nightingale, James; Wang, Qi; Alcaraz Calero, Jose Maria; Grecos, Christos

    2016-04-01

    Software Defined Networks (SDN), when combined with Network Function Virtualization (NFV) represents a paradigm shift in how future networks will behave and be managed. SDN's are expected to provide the underpinning technologies for future innovations such as 5G mobile networks and the Internet of Everything. The SDN architecture offers features that facilitate an abstracted and centralized global network view in which packet forwarding or dropping decisions are based on application flows. Software Defined Networks facilitate a wide range of network management tasks, including the adaptation of real-time video streams as they traverse the network. SHVC, the scalable extension to the recent H.265 standard is a new video encoding standard that supports ultra-high definition video streams with spatial resolutions of up to 7680×4320 and frame rates of 60fps or more. The massive increase in bandwidth required to deliver these U-HD video streams dwarfs the bandwidth requirements of current high definition (HD) video. Such large bandwidth increases pose very significant challenges for network operators. In this paper we go substantially beyond the limited number of existing implementations and proposals for video streaming in SDN's all of which have primarily focused on traffic engineering solutions such as load balancing. By implementing and empirically evaluating an SDN enabled Media Adaptation Network Entity (MANE) we provide a valuable empirical insight into the benefits and limitations of SDN enabled video adaptation for real time video applications. The SDN-MANE is the video adaptation component of our Video Quality Assurance Manager (VQAM) SDN control plane application, which also includes an SDN monitoring component to acquire network metrics and a decision making engine using algorithms to determine the optimum adaptation strategy for any real time video application flow given the current network conditions. Our proposed VQAM application has been implemented and

  4. Real-time Digital Video Watermark Embedding System based on Software in Commodity PC

    Science.gov (United States)

    Yamada, Takaaki; Echizen, Isao; Tezuka, Satoru; Yoshiura, Hiroshi

    Emerging broadband networks and high performance of PCs provide new business opportunities of the live video streaming services for the Internet users in sport events or in music concerts. Digital watermarking for video helps to protect the copyright of the video content and the real-time processing is an essential requirement. For the small start of new business, it should be achieved by flexible software without special equipments. This paper describes a novel real-time watermarking system implemented on a commodity PC. We propose the system architecture and methods to shorten watermarking time by reusing the estimated watermark imperceptibility among neighboring frames. A prototype system enables real time processing in a series of capturing NTSC signals, watermarking the video, encoding it to MPEG4 in QGVA, 1Mbps, 30fps style and storing the video for 12 hours in maximum

  5. Software support for video streaming from smartphone on small airship

    OpenAIRE

    Carretero Rodríguez, Miguel

    2009-01-01

    This project has been created to study and to solve two goals. The main goal has been streaming real video from a smartphone to a laptop and the second goal has been to control the airship electronics from the smartphone. To achieve the main goal of the project, firstly has been necessary realize a technologies study to select the better choice. The chosen technology has been to use of wi-fi, mainly due to the high transmission speed. Once the technology has been chosen, an ad-hoc wi-fi netwo...

  6. The 3D Human Motion Control Through Refined Video Gesture Annotation

    Science.gov (United States)

    Jin, Yohan; Suk, Myunghoon; Prabhakaran, B.

    In the beginning of computer and video game industry, simple game controllers consisting of buttons and joysticks were employed, but recently game consoles are replacing joystick buttons with novel interfaces such as the remote controllers with motion sensing technology on the Nintendo Wii [1] Especially video-based human computer interaction (HCI) technique has been applied to games, and the representative game is 'Eyetoy' on the Sony PlayStation 2. Video-based HCI technique has great benefit to release players from the intractable game controller. Moreover, in order to communicate between humans and computers, video-based HCI is very crucial since it is intuitive, easy to get, and inexpensive. On the one hand, extracting semantic low-level features from video human motion data is still a major challenge. The level of accuracy is really dependent on each subject's characteristic and environmental noises. Of late, people have been using 3D motion-capture data for visualizing real human motions in 3D space (e.g, 'Tiger Woods' in EA Sports, 'Angelina Jolie' in Bear-Wolf movie) and analyzing motions for specific performance (e.g, 'golf swing' and 'walking'). 3D motion-capture system ('VICON') generates a matrix for each motion clip. Here, a column is corresponding to a human's sub-body part and row represents time frames of data capture. Thus, we can extract sub-body part's motion only by selecting specific columns. Different from low-level feature values of video human motion, 3D human motion-capture data matrix are not pixel values, but is closer to human level of semantics.

  7. Meeting radiation therapy patients informational needs through educational videos augmented by 3D visualisation software.

    Science.gov (United States)

    Williams, Katelyn; Blencowe, Jenna; Ind, Melissa; Willis, David

    2017-03-01

    Misconceptions and uncertainties about radiotherapy compound the anxiety patients experience at the commencement of treatment. This project investigated the utility of locally produced treatment process videos in meeting patients' informational needs. In-house video production was conducted on a voluntary basis by staff and patients at a regional Australian radiotherapy centre. Videos included real footage and animated sections created with PEARL(TM) 3D visualisation software (Vertual Ltd, UK) to meet specific key content objectives. Quantitative cross sectional analysis was conducted. Patients attending for simulation watched a relevant video. After their first fraction of radiotherapy they were asked to complete an ethics-reviewed questionnaire about how well the video addressed their information needs. The survey completion rate was 29% (n = 61/212). Surveys were collected over 9 months from August 2014 to April 2015. Statistical analysis found 98% of patients reported that the video was useful in meeting one or more of the learning objectives. Forty-nine percent of patients also reported a reduction in fear and anxiety as a result of watching the video. Patients reported subsequent review of videos at home (39%), primarily to explain treatment processes to loved ones (46%). The combination of real footage and 3D visualisation software assisted in meeting learning objectives regarding the treatment process. Standardised videos provided consistency of information provision to patients and facilitated multiple viewings of the video if desired. © 2017 The Authors. Journal of Medical Radiation Sciences published by John Wiley & Sons Australia, Ltd on behalf of Australian Society of Medical Imaging and Radiation Therapy and New Zealand Institute of Medical Radiation Technology.

  8. Self-evaluation and peer-feedback of medical students' communication skills using a web-based video annotation system. Exploring content and specificity

    NARCIS (Netherlands)

    Hulsman, Robert L.; van der Vloodt, Jane

    2015-01-01

    Objective: Self-evaluation and peer-feedback are important strategies within the reflective practice paradigm for the development and maintenance of professional competencies like medical communication. Characteristics of the self-evaluation and peer-feedback annotations of medical students' video

  9. Creating and Sharing Personalized Time-Based Annotations of Videos on the Web

    NARCIS (Netherlands)

    R.L. Guimarães (Rodrigo); P.S. Cesar Garcia (Pablo Santiago); D.C.A. Bulterman (Dick)

    2010-01-01

    htmlabstractThis paper introduces a multimedia document model that can structure community comments about media. In particular, we describe a set of temporal transformations for multimedia documents that allow end-users to create and share personalized timed-text comments on third party videos. The

  10. Using Linked Data to Annotate and Search Educational Video Resources for Supporting Distance Learning

    Science.gov (United States)

    Yu, Hong Qing; Pedrinaci, C.; Dietze, S.; Domingue, J.

    2012-01-01

    Multimedia educational resources play an important role in education, particularly for distance learning environments. With the rapid growth of the multimedia web, large numbers of educational video resources are increasingly being created by several different organizations. It is crucial to explore, share, reuse, and link these educational…

  11. Overview of the software for the Telemation/Sandia unattended video surveillance system

    Energy Technology Data Exchange (ETDEWEB)

    Merillat, P.D.

    1979-10-01

    A microprocessor has been used to provide the major control functions in the Telemation/Sandia unattended video surveillance system. The software in the microprocessor provides control of the various hardware components and provides the capability of interactive communications with the operator. This document, in conjunction with the commented source listing, defines the philosophy and function of the software. It is assumed that the reader is familiar with the RCA 1802 COSMAC microprocessor and has a reasonable computer science background.

  12. PAPARA(ZZI: An open-source software interface for annotating photographs of the deep-sea

    Directory of Open Access Journals (Sweden)

    Yann Marcon

    2017-01-01

    Full Text Available PAPARA(ZZI is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment. If Internet access is available, PAPARA(ZZI can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS. Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon. These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZI is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

  13. PAPARA(ZZ)I: An open-source software interface for annotating photographs of the deep-sea

    Science.gov (United States)

    Marcon, Yann; Purser, Autun

    PAPARA(ZZ)I is a lightweight and intuitive image annotation program developed for the study of benthic megafauna. It offers functionalities such as free, grid and random point annotation. Annotations may be made following existing classification schemes for marine biota and substrata or with the use of user defined, customised lists of keywords, which broadens the range of potential application of the software to other types of studies (e.g. marine litter distribution assessment). If Internet access is available, PAPARA(ZZ)I can also query and use standardised taxa names directly from the World Register of Marine Species (WoRMS). Program outputs include abundances, densities and size calculations per keyword (e.g. per taxon). These results are written into text files that can be imported into spreadsheet programs for further analyses. PAPARA(ZZ)I is open-source and is available at http://papara-zz-i.github.io. Compiled versions exist for most 64-bit operating systems: Windows, Mac OS X and Linux.

  14. Transana Qualitative Video and Audio Analysis Software as a Tool for Teaching Intellectual Assessment Skills to Graduate Psychology Students

    Science.gov (United States)

    Rush, S. Craig

    2014-01-01

    This article draws on the author's experience using qualitative video and audio analysis, most notably through use of the Transana qualitative video and audio analysis software program, as an alternative method for teaching IQ administration skills to students in a graduate psychology program. Qualitative video and audio analysis may be useful for…

  15. Validation of a Video Analysis Software Package for Quantifying Movement Velocity in Resistance Exercises.

    Science.gov (United States)

    Sañudo, Borja; Rueda, David; Pozo-Cruz, Borja Del; de Hoyo, Moisés; Carrasco, Luis

    2016-10-01

    Sañudo, B, Rueda, D, del Pozo-Cruz, B, de Hoyo, M, and Carrasco, L. Validation of a video analysis software package for quantifying movement velocity in resistance exercises. J Strength Cond Res 30(10): 2934-2941, 2016-The aim of this study was to establish the validity of a video analysis software package in measuring mean propulsive velocity (MPV) and the maximal velocity during bench press. Twenty-one healthy males (21 ± 1 year) with weight training experience were recruited, and the MPV and the maximal velocity of the concentric phase (Vmax) were compared with a linear position transducer system during a standard bench press exercise. Participants performed a 1 repetition maximum test using the supine bench press exercise. The testing procedures involved the simultaneous assessment of bench press propulsive velocity using 2 kinematic (linear position transducer and semi-automated tracking software) systems. High Pearson's correlation coefficients for MPV and Vmax between both devices (r = 0.473 to 0.993) were observed. The intraclass correlation coefficients for barbell velocity data and the kinematic data obtained from video analysis were high (>0.79). In addition, the low coefficients of variation indicate that measurements had low variability. Finally, Bland-Altman plots with the limits of agreement of the MPV and Vmax with different loads showed a negative trend, which indicated that the video analysis had higher values than the linear transducer. In conclusion, this study has demonstrated that the software used for the video analysis was an easy to use and cost-effective tool with a very high degree of concurrent validity. This software can be used to evaluate changes in velocity of training load in resistance training, which may be important for the prescription and monitoring of training programmes.

  16. Basic Principle and Application of Video Recovery Software for “Dahua” and “Hikvision” Brand

    Directory of Open Access Journals (Sweden)

    Yang Fan

    2015-01-01

    Full Text Available This article describes the basic principle of mainstream video recovery software in “Dahua” and “Hikvision” brand for the current market, and introduces a practical method to use this software to abstract the digital video, especially the detailed description of application experience of carrying out video abstraction for hard disk with part of damaged sector, and finally make a summary.

  17. Stereoscopic video and the quest for virtual reality: an annotated bibliography of selected topics

    Science.gov (United States)

    Starks, Michael R.

    1991-08-01

    It is the aim of most work with graphics photography and video to create vivid and compelling images. Though telepresence and virtual reality are new terms there exists a vast body of research in stereoscopic vido and other fields with similar objectives. Most of this work has appeared in patent documents or obscure publications and is rarely cited. In order to stimulate research a number of areas of interest are briefly reviewed and accompanied by extensive bibliographies. These include single camera and dual camera stereoscopy cornpatible 3D recording and transmission helmet mounted displays field sequential stereo and head and eyetracking devices.

  18. Towards a ground truth of AADT on using video data and tracking software?

    DEFF Research Database (Denmark)

    Øhlenschlæger, Rasmus; Lahrmann, Harry Spaabæk; B. Moeslund, Thomas

    to measure traffic volumes are increasingly used, but there is limited documentation on the reliability of these. This paper compares manual registrations, treated as ground truth, the hardware independent software RUBA and an on-the-shelf product. While the RUBA software, in general, had a reasonable......There is an increase in traffic volumes and, as such, a requirement for maximisation of the road capacity. It is crucial that there is awareness of the traffic volumes in order to make the right choices regarding road development. Video registrations and related software to video analysis...... precision on the direction parallel to the camera direction (8% and 3% deviations, respectively); it was less precise regarding transversal-driving vehicles (23% deviation). The on-the-shelf hardware had a significantly higher deviation regarding the two parallel directions, (35% and 67% deviations...

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

    Science.gov (United States)

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

    2018-01-01

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

  20. Improving Video Game Development: Facilitating Heterogeneous Team Collaboration through Flexible Software Processes

    Science.gov (United States)

    Musil, Juergen; Schweda, Angelika; Winkler, Dietmar; Biffl, Stefan

    Based on our observations of Austrian video game software development (VGSD) practices we identified a lack of systematic processes/method support and inefficient collaboration between various involved disciplines, i.e. engineers and artists. VGSD includes heterogeneous disciplines, e.g. creative arts, game/content design, and software. Nevertheless, improving team collaboration and process support is an ongoing challenge to enable a comprehensive view on game development projects. Lessons learned from software engineering practices can help game developers to increase game development processes within a heterogeneous environment. Based on a state of the practice survey in the Austrian games industry, this paper presents (a) first results with focus on process/method support and (b) suggests a candidate flexible process approach based on Scrum to improve VGSD and team collaboration. Results showed (a) a trend to highly flexible software processes involving various disciplines and (b) identified the suggested flexible process approach as feasible and useful for project application.

  1. Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

    Science.gov (United States)

    Brunner, J; Krummenauer, F; Lehr, H A

    2000-04-01

    Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

  2. Software Optimization of Video Codecs on Pentium Processor with MMX Technology

    Directory of Open Access Journals (Sweden)

    Liu KJ Ray

    2001-01-01

    Full Text Available A key enabling technology for the proliferation of multimedia PC's is the availability of fast video codecs, which are the basic building blocks of many new multimedia applications. Since most industrial video coding standards (e.g., MPEG1, MPEG2, H.261, H.263 only specify the decoder syntax, there are a lot of rooms for optimization in a practical implementation. When considering a specific hardware platform like the PC, the algorithmic optimization must be considered in tandem with the architecture of the PC. Specifically, an algorithm that is optimal in the sense of number of operations needed may not be the fastest implementation on the PC. This is because special instructions are available which can perform several operations at once under special circumstances. In this work, we describe a fast implementation of H.263 video encoder for the Pentium processor with MMX technology. The described codec is adopted for video mail and video phone softwares used in IBM ThinkPad.

  3. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

    Science.gov (United States)

    Eisenhaber, Birgit; Kuchibhatla, Durga; Sherman, Westley; Sirota, Fernanda L; Berezovsky, Igor N; Wong, Wing-Cheong; Eisenhaber, Frank

    2016-01-01

    As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction.

  4. Development of a Kinect Software Tool to Classify Movements during Active Video Gaming.

    Directory of Open Access Journals (Sweden)

    Michael Rosenberg

    Full Text Available While it has been established that using full body motion to play active video games results in increased levels of energy expenditure, there is little information on the classification of human movement during active video game play in relationship to fundamental movement skills. The aim of this study was to validate software utilising Kinect sensor motion capture technology to recognise fundamental movement skills (FMS, during active video game play. Two human assessors rated jumping and side-stepping and these assessments were compared to the Kinect Action Recognition Tool (KART, to establish a level of agreement and determine the number of movements completed during five minutes of active video game play, for 43 children (m = 12 years 7 months ± 1 year 6 months. During five minutes of active video game play, inter-rater reliability, when examining the two human raters, was found to be higher for the jump (r = 0.94, p < .01 than the sidestep (r = 0.87, p < .01, although both were excellent. Excellent reliability was also found between human raters and the KART system for the jump (r = 0.84, p, .01 and moderate reliability for sidestep (r = 0.6983, p < .01 during game play, demonstrating that both humans and KART had higher agreement for jumps than sidesteps in the game play condition. The results of the study provide confidence that the Kinect sensor can be used to count the number of jumps and sidestep during five minutes of active video game play with a similar level of accuracy as human raters. However, in contrast to humans, the KART system required a fraction of the time to analyse and tabulate the results.

  5. Let's Meet at the Mobile - Learning Dialogs with a Video Conferencing Software for Mobile Devices

    Directory of Open Access Journals (Sweden)

    Hans L. Cycon

    2009-07-01

    Full Text Available Mobile phones and related gadgets in networks are omnipresent at our students, advertising itself as the platform for mobile, pervasive learning. Currently, these devices rapidly open and enhance, being soon able to serve as a major platform for rich, open multimedia applications and communication. In this report we introduce a video conferencing software, which seamlessly integrates mobile with stationary users into fully distributed multi-party conversations. Following the paradigm of flexible, user-initiated group communication, we present an integrated solution, which scales well for medium-size conferences and accounts for the heterogeneous nature of mobile and stationary participants. This approach allows for a spontaneous, location independent establishment of video dialogs, which is of particular importance in interactive learning scenarios. The work is based on a highly optimized realization of a H.264 codec.

  6. Real time video processing software for the analysis of endoscopic guided-biopsies

    Science.gov (United States)

    Ordoñez, C.; Bouchet, A.; Pastore, J.; Blotta, E.

    2011-12-01

    The severity in Barrett esophagus disease is, undoubtedly, the possibility of its malignization. To make an early diagnosis in order to avoid possible complications, it is absolutely necessary collect biopsies to make a histological analysis. This should be done under endoscopic control to avoid mucus areas that may co-exist within the columnar epithelial, which could lead to a false diagnosis. This paper presents a video processing software in real-time in order to delineate and enhance areas of interest to facilitate the work of the expert.

  7. Real-time video streaming of sonographic clips using domestic internet networks and free videoconferencing software.

    Science.gov (United States)

    Liteplo, Andrew S; Noble, Vicki E; Attwood, Ben H C

    2011-11-01

    As the use of point-of-care sonography spreads, so too does the need for remote expert over-reading via telesonogrpahy. We sought to assess the feasibility of using familiar, widespread, and cost-effective existent technology to allow remote over-reading of sonograms in real time and to compare 4 different methods of transmission and communication for both the feasibility of transmission and image quality. Sonographic video clips were transmitted using 2 different connections (WiFi and 3G) and via 2 different videoconferencing modalities (iChat [Apple Inc, Cupertino, CA] and Skype [Skype Software Sàrl, Luxembourg]), for a total of 4 different permutations. The clips were received at a remote location and recorded and then scored by expert reviewers for image quality, resolution, and detail. Wireless transmission of sonographic clips was feasible in all cases when WiFi was used and when Skype was used over a 3G connection. Images transmitted via a WiFi connection were statistically superior to those transmitted via 3G in all parameters of quality (average P = .031), and those sent by iChat were superior to those sent by Skype but not statistically so (average P = .057). Wireless transmission of sonographic video clips using inexpensive hardware, free videoconferencing software, and domestic Internet networks is feasible with retention of image quality sufficient for interpretation. WiFi transmission results in greater image quality than transmission by a 3G network.

  8. ALGORITHM OF PLACEMENT OF VIDEO SURVEILLANCE CAMERAS AND ITS SOFTWARE IMPLEMENTATION

    Directory of Open Access Journals (Sweden)

    Loktev Alexey Alexeevich

    2012-10-01

    Full Text Available Comprehensive distributed safety, control, and monitoring systems applied by companies and organizations of different ownership structure play a substantial role in the present-day society. Video surveillance elements that ensure image processing and decision making in automated or automatic modes are the essential components of new systems. This paper covers the modeling of video surveillance systems installed in buildings, and the algorithm, or pattern, of video camera placement with due account for nearly all characteristics of buildings, detection and recognition facilities, and cameras themselves. This algorithm will be subsequently implemented as a user application. The project contemplates a comprehensive approach to the automatic placement of cameras that take account of their mutual positioning and compatibility of tasks. The project objective is to develop the principal elements of the algorithm of recognition of a moving object to be detected by several cameras. The image obtained by different cameras will be processed. Parameters of motion are to be identified to develop a table of possible options of routes. The implementation of the recognition algorithm represents an independent research project to be covered by a different article. This project consists in the assessment of the degree of complexity of an algorithm of camera placement designated for identification of cases of inaccurate algorithm implementation, as well as in the formulation of supplementary requirements and input data by means of intercrossing sectors covered by neighbouring cameras. The project also contemplates identification of potential problems in the course of development of a physical security and monitoring system at the stage of the project design development and testing. The camera placement algorithm has been implemented as a software application that has already been pilot tested on buildings and inside premises that have irregular dimensions. The

  9. Dependency Tree Annotation Software

    Science.gov (United States)

    2015-11-01

    CoNLL is organized by the Association for Computational Linguistics (ACL) Special Interest Group on Natural Language Learning (SIGNLL). 2. Features...The system supports interactive visualization and editing of dependency trees—a formalism frequently used in computational linguistics to represent...between words. DTE supports the widely used Conference on Computational Natural Language Learning (CoNLL)-X format as well as several other file

  10. Sexual content in video games: an analysis of the Entertainment Software Rating Board classification from 1994 to 2013.

    Science.gov (United States)

    Vidaña-Pérez, Dèsirée; Braverman-Bronstein, Ariela; Basto-Abreu, Ana; Barrientos-Gutierrez, Inti; Hilscher, Rainer; Barrientos-Gutierrez, Tonatiuh

    2018-01-11

    Background: Video games are widely used by children and adolescents and have become a significant source of exposure to sexual content. Despite evidence of the important role of media in the development of sexual attitudes and behaviours, little attention has been paid to monitor sexual content in video games. Methods: Data was obtained about sexual content and rating for 23722 video games from 1994 to 2013 from the Entertainment Software Rating Board database; release dates and information on the top 100 selling video games was also obtained. A yearly prevalence of sexual content according to rating categories was calculated. Trends and comparisons were estimated using Joinpoint regression. Results: Sexual content was present in 13% of the video games. Games rated 'Mature' had the highest prevalence of sexual content (34.5%) followed by 'Teen' (30.7%) and 'E10+' (21.3%). Over time, sexual content decreased in the 'Everyone' category, 'E10+' maintained a low prevalence and 'Teen' and 'Mature' showed a marked increase. Both top and non-top video games showed constant increases, with top selling video games having 10.1% more sexual content across the period of study. Conclusion: Over the last 20 years, the prevalence of sexual content has increased in video games with a 'Teen' or 'Mature' rating. Further studies are needed to quantify the potential association between sexual content in video games and sexual behaviour in children and adolescents.

  11. A flexible software architecture for scalable real-time image and video processing applications

    Science.gov (United States)

    Usamentiaga, Rubén; Molleda, Julio; García, Daniel F.; Bulnes, Francisco G.

    2012-06-01

    Real-time image and video processing applications require skilled architects, and recent trends in the hardware platform make the design and implementation of these applications increasingly complex. Many frameworks and libraries have been proposed or commercialized to simplify the design and tuning of real-time image processing applications. However, they tend to lack flexibility because they are normally oriented towards particular types of applications, or they impose specific data processing models such as the pipeline. Other issues include large memory footprints, difficulty for reuse and inefficient execution on multicore processors. This paper presents a novel software architecture for real-time image and video processing applications which addresses these issues. The architecture is divided into three layers: the platform abstraction layer, the messaging layer, and the application layer. The platform abstraction layer provides a high level application programming interface for the rest of the architecture. The messaging layer provides a message passing interface based on a dynamic publish/subscribe pattern. A topic-based filtering in which messages are published to topics is used to route the messages from the publishers to the subscribers interested in a particular type of messages. The application layer provides a repository for reusable application modules designed for real-time image and video processing applications. These modules, which include acquisition, visualization, communication, user interface and data processing modules, take advantage of the power of other well-known libraries such as OpenCV, Intel IPP, or CUDA. Finally, we present different prototypes and applications to show the possibilities of the proposed architecture.

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

    Science.gov (United States)

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

    2015-09-01

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

  13. Measuring fish and their physical habitats: Versatile 2D and 3D video techniques with user-friendly software

    Science.gov (United States)

    Neuswanger, Jason R.; Wipfli, Mark S.; Rosenberger, Amanda E.; Hughes, Nicholas F.

    2017-01-01

    Applications of video in fisheries research range from simple biodiversity surveys to three-dimensional (3D) measurement of complex swimming, schooling, feeding, and territorial behaviors. However, researchers lack a transparently developed, easy-to-use, general purpose tool for 3D video measurement and event logging. Thus, we developed a new measurement system, with freely available, user-friendly software, easily obtained hardware, and flexible underlying mathematical methods capable of high precision and accuracy. The software, VidSync, allows users to efficiently record, organize, and navigate complex 2D or 3D measurements of fish and their physical habitats. Laboratory tests showed submillimetre accuracy in length measurements of 50.8 mm targets at close range, with increasing errors (mostly animal behavior and ecology.

  14. The development of learning video media based on swishmax and screencast o-matic softwares through the contextual approach

    Directory of Open Access Journals (Sweden)

    Siti Kholifah

    2017-01-01

    Full Text Available The low learning outcomes as a result of low students’ interest in learning on the Organizational Behavior subject was the background of the study. The objective of the study was to develop a learning media video based on swishmax dan screencast o-matic softwares through the contextual approach. The study used the ADDIE development model which consisted of five stages: Analysis, Design, Development, Implementation, and Evaluation. Before using, the learning video media first tested  by the media experts and the subject experts. Then; it needed students’ feedback on questionnaires about the media. The results of the  experts, and students’ questionnaires showed that the media was very good and feasible to be used. The effectiveness of the media was analyzed by t-test. It obtained the mean score of experimental class was 85.03; whereas the mean score of control class was only 79.00. By using the t test scores was 3.30> 1.997; then Ho was rejected. Therefore; it can be concluded that learning by using the learning video media based swishmax and screencast o-matic softwares through the contextual approach was better than the conventional teaching on Organizational Behavior.Rendahnya hasil belajar sebagai akibat dari rendahnya minat belajar mahasiswa pada mata kuliah perilaku organisasi adalah hal yang mendasari dilakukannya penelitian ini. Penelitian ini bertujuan untuk mengembangkan media video pembelajaran berbasis Software Swishmax dan Screencast O-matic dengan pendekatan kontekstual. Pada penelitian ini menggunakan model pengembangan ADDIE dimana dalam tahapnya terdiri dari 5 tahapan yaitu analisis, desain, development, implementasi, evaluasi. Sebelum digunakan, media video pembelajaran terlebih dahulu dilakukan uji validasi oleh ahli media dan ahli materi. Selain itu diperlukan juga angket tanggapan mahasiswa mengenai media tersebut. Hasil dari validasi ahli media, materi dan angket mahasiswa berkriteria sangat baik dan layak untuk

  15. A pilot study of the Video Observations Aarts and Aarts (VOAA) a new software program to measure motor behaviour in children with cerebral palsy

    NARCIS (Netherlands)

    Aarts, Pauline BM; Jongerius, Peter H; Aarts, Michel AG; Van Hartingsveldt, Margo J; Anderson, Patricia G; Beumer, Annechien

    2007-01-01

    A new computer software program to score video observations, Video Observations Aarts and Aarts (VOAA) was developed to evaluate paediatric occupational therapy interventions. The VOAA is an observation tool that assesses the frequency, duration and quality of arm/hand use in children, in particular

  16. A pilot study of the Video Observations Aarts and Aarts (VOAA): a new software program to measure motor behaviour in children with cerebral palsy.

    NARCIS (Netherlands)

    Aarts, P.B.; Jongerius, P.H.; Aarts, M.A.; Hartingsveldt, M.J. van; Anderson, P.G.; Beumer, A.

    2007-01-01

    A new computer software program to score video observations, Video Observations Aarts and Aarts (VOAA) was developed to evaluate paediatric occupational therapy interventions. The VOAA is an observation tool that assesses the frequency, duration and quality of arm/hand use in children, in particular

  17. Zoneminder as ‘Software as a Service’ and Load Balancing of Video Surveillance Requests

    DEFF Research Database (Denmark)

    Deshmukh, Aaradhana A.; Mihovska, Albena D.; Prasad, Ramjee

    2012-01-01

    Cloud computing is evolving as a key computing platform for sharing resources that include infrastructures, softwares, applications, and business processes. Virtualization is a core technology for enabling cloud resource sharing. Software as a Service (SaaS) on the cloud platform provides softwar...

  18. Computing human image annotation.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities.

  19. Measurement and processing of signatures in the visible range using a calibrated video camera and the CAMDET software package

    Science.gov (United States)

    Sheffer, Dan

    1997-06-01

    A procedure for calibration of a color video camera has been developed at EORD. The RGB values of standard samples, together with the spectral radiance values of the samples, are used to calculate a transformation matrix between the RGB and CIEXYZ color spaces. The transformation matrix is then used to calculate the XYZ color coordinates of distant objects imaged in the field. These, in turn, are used in order to calculate the CIELAB color coordinates of the objects. Good agreement between the calculated coordinates and those obtained from spectroradiometric data is achieved. Processing of the RGB values of pixels in the digital image of a scene using the CAMDET software package which was developed at EORD, results in `Painting Maps' in which the true apparent CIELAB color coordinates are used. The paper discusses the calibration procedure, its advantages and shortcomings and suggests a definition for the visible signature of objects. The Camdet software package is described and some examples are given.

  20. The Study on Neuro-IE Management Software in Manufacturing Enterprises. -The Application of Video Analysis Technology

    Science.gov (United States)

    Bian, Jun; Fu, Huijian; Shang, Qian; Zhou, Xiangyang; Ma, Qingguo

    This paper analyzes the outstanding problems in current industrial production by reviewing the three stages of the Industrial Engineering Development. Based on investigations and interviews in enterprises, we propose the new idea of applying "computer video analysis technology" to new industrial engineering management software, and add "loose-coefficient" of the working station to this software in order to arrange scientific and humanistic production. Meanwhile, we suggest utilizing Biofeedback Technology to promote further research on "the rules of workers' physiological, psychological and emotional changes in production". This new kind of combination will push forward industrial engineering theories and benefit enterprises in progressing towards flexible social production, thus it will be of great theory innovation value, social significance and application value.

  1. Hardware/Software Issues for Video Guidance Systems: The Coreco Frame Grabber

    Science.gov (United States)

    Bales, John W.

    1996-01-01

    The F64 frame grabber is a high performance video image acquisition and processing board utilizing the TMS320C40 and TMS34020 processors. The hardware is designed for the ISA 16 bit bus and supports multiple digital or analog cameras. It has an acquisition rate of 40 million pixels per second, with a variable sampling frequency of 510 kHz to MO MHz. The board has a 4MB frame buffer memory expandable to 32 MB, and has a simultaneous acquisition and processing capability. It supports both VGA and RGB displays, and accepts all analog and digital video input standards.

  2. Prying into the intimate secrets of animal lives; software beyond hardware for comprehensive annotation in 'Daily Diary' tags.

    Science.gov (United States)

    Walker, James S; Jones, Mark W; Laramee, Robert S; Holton, Mark D; Shepard, Emily Lc; Williams, Hannah J; Scantlebury, D Michael; Marks, Nikki J; Magowan, Elizabeth A; Maguire, Iain E; Bidder, Owen R; Di Virgilio, Agustina; Wilson, Rory P

    2015-01-01

    Smart tags attached to freely-roaming animals recording multiple parameters at infra-second rates are becoming commonplace, and are transforming our understanding of the way wild animals behave. Interpretation of such data is complex and currently limits the ability of biologists to realise the value of their recorded information. This work presents Framework4, an all-encompassing software suite which operates on smart sensor data to determine the 4 key elements considered pivotal for movement analysis from such tags (Endangered Species Res 4: 123-37, 2008). These are; animal trajectory, behaviour, energy expenditure and quantification of the environment in which the animal moves. The program transforms smart sensor data into dead-reckoned movements, template-matched behaviours, dynamic body acceleration-derived energetics and position-linked environmental data before outputting it all into a single file. Biologists are thus left with a single data set where animal actions and environmental conditions can be linked across time and space. Framework4 is a user-friendly software that assists biologists in elucidating 4 key aspects of wild animal ecology using data derived from tags with multiple sensors recording at high rates. Its use should enhance the ability of biologists to derive meaningful data rapidly from complex data.

  3. Ground Truth Annotation in T Analyst

    DEFF Research Database (Denmark)

    2015-01-01

    This video shows how to annotate the ground truth tracks in the thermal videos. The ground truth tracks are produced to be able to compare them to tracks obtained from a Computer Vision tracking approach. The program used for annotation is T-Analyst, which is developed by Aliaksei Laureshyn, Ph...

  4. Droplet morphometry and velocimetry (DMV): a video processing software for time-resolved, label-free tracking of droplet parameters.

    Science.gov (United States)

    Basu, Amar S

    2013-05-21

    Emerging assays in droplet microfluidics require the measurement of parameters such as drop size, velocity, trajectory, shape deformation, fluorescence intensity, and others. While micro particle image velocimetry (μPIV) and related techniques are suitable for measuring flow using tracer particles, no tool exists for tracking droplets at the granularity of a single entity. This paper presents droplet morphometry and velocimetry (DMV), a digital video processing software for time-resolved droplet analysis. Droplets are identified through a series of image processing steps which operate on transparent, translucent, fluorescent, or opaque droplets. The steps include background image generation, background subtraction, edge detection, small object removal, morphological close and fill, and shape discrimination. A frame correlation step then links droplets spanning multiple frames via a nearest neighbor search with user-defined matching criteria. Each step can be individually tuned for maximum compatibility. For each droplet found, DMV provides a time-history of 20 different parameters, including trajectory, velocity, area, dimensions, shape deformation, orientation, nearest neighbour spacing, and pixel statistics. The data can be reported via scatter plots, histograms, and tables at the granularity of individual droplets or by statistics accrued over the population. We present several case studies from industry and academic labs, including the measurement of 1) size distributions and flow perturbations in a drop generator, 2) size distributions and mixing rates in drop splitting/merging devices, 3) efficiency of single cell encapsulation devices, 4) position tracking in electrowetting operations, 5) chemical concentrations in a serial drop dilutor, 6) drop sorting efficiency of a tensiophoresis device, 7) plug length and orientation of nonspherical plugs in a serpentine channel, and 8) high throughput tracking of >250 drops in a reinjection system. Performance metrics

  5. Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

    Science.gov (United States)

    Jedlovec, G.; Srikishen, J.; Edwards, R.; Cross, D.; Welch, J. D.; Smith, M. R.

    2013-12-01

    The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of 'big data' available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Short-term Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video

  6. Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

    Science.gov (United States)

    Jedlovec, Gary; Srikishen, Jayanthi; Edwards, Rita; Cross, David; Welch, Jon; Smith, Matt

    2013-01-01

    The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of "big data" available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Shortterm Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video

  7. Software

    Energy Technology Data Exchange (ETDEWEB)

    Macedo, R.; Budd, G.; Ross, E.; Wells, P.

    2010-07-15

    The software section of this journal presented new software programs that have been developed to help in the exploration and development of hydrocarbon resources. Software provider IHS Inc. has made additions to its geological and engineering analysis software tool, IHS PETRA, a product used by geoscientists and engineers to visualize, analyze and manage well production, well log, drilling, reservoir, seismic and other related information. IHS PETRA also includes a directional well module and a decline curve analysis module to improve analysis capabilities in unconventional reservoirs. Petris Technology Inc. has developed a software to help manage the large volumes of data. PetrisWinds Enterprise (PWE) helps users find and manage wellbore data, including conventional wireline and MWD core data; analysis core photos and images; waveforms and NMR; and external files documentation. Ottawa-based Ambercore Software Inc. has been collaborating with Nexen on the Petroleum iQ software for steam assisted gravity drainage (SAGD) producers. Petroleum iQ integrates geology and geophysics data with engineering data in 3D and 4D. Calgary-based Envirosoft Corporation has developed a software that reduces the costly and time-consuming effort required to comply with Directive 39 of the Alberta Energy Resources Conservation Board. The product includes an emissions modelling software. Houston-based Seismic Micro-Technology (SMT) has developed the Kingdom software that features the latest in seismic interpretation. Holland-based Joa Oil and Gas and Calgary-based Computer Modelling Group have both supplied the petroleum industry with advanced reservoir simulation software that enables reservoir interpretation. The 2010 software survey included a guide to new software applications designed to facilitate petroleum exploration, drilling and production activities. Oil and gas producers can use the products for a range of functions, including reservoir characterization and accounting. In

  8. "Market and Strategy of the Home Video-Game Software in the U.S. --- Brief Comparison with Japan ---"(in Japanese)

    OpenAIRE

    Junjiro Shintaku; Fumihiko Ikuine

    2001-01-01

    The purpose of this research is to reveal the characteristics of the Home Video-Game industry of the United States and to examine the reason why Japanese software publishers don't fully succeed in the US market. First, we report the present state of US Home Video-Game industry, and then make a brief comparison between the US and Japan regarding the management of software publishers. As the result of our investigation, we found that as opposed to the Japanese market, the US market is character...

  9. Musculo-skeletal Disorders among Video Display Terminal Users: A Cross-Sectional Study in a Software Company, Kolkata.

    Science.gov (United States)

    Basu, Rivu; Dasgupta, Aparajita; Ghosal, Gautam

    2014-12-01

    IT has revolutionized economies throughout the world, more so in India. West Bengal has also got its share of IT boom. But with this, it has brought in the class of human resource of Video Display Terminal workers operators that and along with that can cause a host of occupational problems in them namely musculoskeletal, ocular and psychological systems. The current study had assessed some of the musculoskeletal disorders occurring due to VIDEO DISPLAY TERMINAL use. An analytical cross-sectional study was done in a Software Company of Sector V, Kolkata, the IT hub of West Bengal. Of all the employees, required sample size of 206 was selected by Simple Random Sampling. After proper permissions and consent, socio-demographic variables were collected by standardized instruments, musculoskeletal morbidity was collected by Nordic questionnaire, and ergonomic practices were obtained by checklists. 90.78% of population showed some form of musculo skeletal symptoms. They were highest in fingers, elbows, wrist, shoulder, upper, while legs and lower back showed low morbidities. Increasing age, female sex, increasing years of work, repetition of work, poorer ergonomic scores all showed to have increased the symptoms. The regionwise ergonomic scores revealed how the poorer scores affected the musculo skeletal systems adversely. Several individual adverse ergonomic practices were also elicited. The study goes hand to hand with many other studies throughout the world and also in India. However, a much higher morbidity has been found in this study probably due to a symptom based questionnaire. The adverse practices obtained here goes well with other relevant studies. This study puts occupational health problems of VIDEO DISPLAY TERMINAL users, and upholds the need of future multicentric cohort studies along with implementation of proper measures to ameliorate the effects of this occupational hazard.

  10. Musculo-skeletal Disorders among Video Display Terminal Users: A Cross-Sectional Study in a Software Company, Kolkata

    Science.gov (United States)

    Dasgupta, Aparajita; Ghosal, Gautam

    2014-01-01

    Introduction: IT has revolutionized economies throughout the world, more so in India. West Bengal has also got its share of IT boom. But with this, it has brought in the class of human resource of Video Display Terminal workers operators that and along with that can cause a host of occupational problems in them namely musculoskeletal, ocular and psychological systems. The current study had assessed some of the musculoskeletal disorders occurring due to VIDEO DISPLAY TERMINAL use. Materials and Methods: An analytical cross-sectional study was done in a Software Company of Sector V, Kolkata, the IT hub of West Bengal. Of all the employees, required sample size of 206 was selected by Simple Random Sampling. After proper permissions and consent, socio-demographic variables were collected by standardized instruments, musculoskeletal morbidity was collected by Nordic questionnaire, and ergonomic practices were obtained by checklists. Results: 90.78% of population showed some form of musculo skeletal symptoms. They were highest in fingers, elbows, wrist, shoulder, upper, while legs and lower back showed low morbidities. Increasing age, female sex, increasing years of work, repetition of work, poorer ergonomic scores all showed to have increased the symptoms. The regionwise ergonomic scores revealed how the poorer scores affected the musculo skeletal systems adversely. Several individual adverse ergonomic practices were also elicited. Discussion: The study goes hand to hand with many other studies throughout the world and also in India. However, a much higher morbidity has been found in this study probably due to a symptom based questionnaire. The adverse practices obtained here goes well with other relevant studies. Conclusion: This study puts occupational health problems of VIDEO DISPLAY TERMINAL users, and upholds the need of future multicentric cohort studies along with implementation of proper measures to ameliorate the effects of this occupational hazard. PMID

  11. A Dynamic Reconfigurable Hardware/Software Architecture for Object Tracking in Video Streams

    Directory of Open Access Journals (Sweden)

    Christophe Bobda

    2006-10-01

    Full Text Available This paper presents the design and implementation of a feature tracker on an embedded reconfigurable hardware system. Contrary to other works, the focus here is on the efficient hardware/software partitioning of the feature tracker algorithm, a viable data flow management, as well as an efficient use of memory and processor features. The implementation is done on a Xilinx Spartan 3 evaluation board and the results provided show the superiority of our implementation compared to the other works.

  12. A Dynamic Reconfigurable Hardware/Software Architecture for Object Tracking in Video Streams

    Directory of Open Access Journals (Sweden)

    Mühlbauer Felix

    2006-01-01

    Full Text Available This paper presents the design and implementation of a feature tracker on an embedded reconfigurable hardware system. Contrary to other works, the focus here is on the efficient hardware/software partitioning of the feature tracker algorithm, a viable data flow management, as well as an efficient use of memory and processor features. The implementation is done on a Xilinx Spartan 3 evaluation board and the results provided show the superiority of our implementation compared to the other works.

  13. Digital video.

    Science.gov (United States)

    Johnson, Don; Johnson, Mike

    2004-04-01

    The process of digital capture, editing, and archiving video has become an important aspect of documenting arthroscopic surgery. Recording the arthroscopic findings before and after surgery is an essential part of the patient's medical record. The hardware and software has become more reasonable to purchase, but the learning curve to master the software is steep. Digital video is captured at the time of arthroscopy to a hard disk, and written to a CD at the end of the operative procedure. The process of obtaining video of open procedures is more complex. Outside video of the procedure is recorded on digital tape with a digital video camera. The camera must be plugged into a computer to capture the video on the hard disk. Adobe Premiere software is used to edit the video and render the finished video to the hard drive. This finished video is burned onto a CD. We outline the choice of computer hardware and software for the manipulation of digital video. The techniques of backup and archiving the completed projects and files also are outlined. The uses of digital video for education and the formats that can be used in PowerPoint presentations are discussed.

  14. A hardware/software simulation for the video tracking system of the Kuiper Airborne Observatory telescope

    Science.gov (United States)

    Boozer, G. A.; Mckibbin, D. D.; Haas, M. R.; Erickson, E. F.

    1984-01-01

    This simulator was created so that C-141 Kuiper Airborne Observatory investigators could test their Airborne Data Acquisition and Management System software on a system which is generally more accessible than the ADAMS on the plane. An investigator can currently test most of his data acquisition program using the data computer simulator in the Cave. (The Cave refers to the ground-based computer facilities for the KAO and the associated support personnel.) The main Cave computer is interfaced to the data computer simulator in order to simulate the data-Exec computer communications. However until now, there has been no way to test the data computer interface to the tracker. The simulator described here simulates both the KAO Exec and tracker computers with software which runs on the same Hewlett-Packard (HP) computer as the investigator's data acquisition program. A simulator control box is hardwired to the computer to provide monitoring of tracker functions, to provide an operator panel similar to the real tracker, and to simulate the 180 deg phase shifting of the chopper squre-wave reference with beam switching. If run in the Cave, one can use their Exec simulator and this tracker simulator.

  15. Manual Whisker Annotator (MWA: A Modular Open-Source Tool

    Directory of Open Access Journals (Sweden)

    Brett M. Hewitt

    2016-04-01

    Full Text Available Rodents are key to generating translational data for healthcare research. Behavioural analyses, in particular, are integral to the non-invasive monitoring of rodent health and welfare. Finding quantitative behavioural measures mitigates stress, allowing for the animal behave freely while also enabling the same animal to be studied over the time-course of its life. Locomotion and whisking are both such quantitative behavioural measures, and have been found to be significantly impacted in rodent models of neurodegenerative disease. While automatic trackers of whiskers and locomotion exist, a manual tracker is required to validate these approaches, and also to annotate complex videos where these automatic versions fail. Manually annotating whiskers for research purposes is a long and tedious task and current software does little to provide an intuitive and simple interface to carry out this task. This led to the creation of the Manual Whisker Annotator (MWA. MWA is an open source, portable whisker annotation tool developed for the Windows platform. Not only does MWA make the process much quicker, it also provides added statistical tools to analyse the data. MWA was developed in C# and WPF using the .NET framework, and could be used in any situation where annotating or tracking multiple targets is desired.

  16. Motion lecture annotation system to learn Naginata performances

    Science.gov (United States)

    Kobayashi, Daisuke; Sakamoto, Ryota; Nomura, Yoshihiko

    2013-12-01

    This paper describes a learning assistant system using motion capture data and annotation to teach "Naginata-jutsu" (a skill to practice Japanese halberd) performance. There are some video annotation tools such as YouTube. However these video based tools have only single angle of view. Our approach that uses motion-captured data allows us to view any angle. A lecturer can write annotations related to parts of body. We have made a comparison of effectiveness between the annotation tool of YouTube and the proposed system. The experimental result showed that our system triggered more annotations than the annotation tool of YouTube.

  17. Evaluating sub-lethal effects of orchard-applied pyrethroids using video-tracking software to quantify honey bee behaviors.

    Science.gov (United States)

    Ingram, Erin M; Augustin, Julie; Ellis, Marion D; Siegfried, Blair D

    2015-09-01

    Managed honey bee, Apis mellifera L., colonies are contracted to pollinate fruit and nut orchards improving crop quality and yield. Colonies placed in orchards are potentially exposed to pyrethroid insecticides used for broad-spectrum pest control. Pyrethroids have been reported to pose minimal risk to bees due to their low application rates in the field and putative repellent properties. This repellency is believed to alter foraging behavior with the benefit of preventing bees from encountering a lethal dose in the field. However, sub-lethal exposure to pyrethroids may adversely impact bee behavior potentially resulting in social dysfunction or disruption of foraging. This study quantified behaviors associated with sub-lethal exposure to orchard-applied pyrethroids including, lambda-cyhalothrin, esfenvalerate, and permethrin, using video tracking software, Ethovision XT (Noldus Information Technologies). Bee locomotion, social interaction, and time spent near a food source were measured over a 24-h period. Bees treated with a pyrethroid traveled 30-71% less than control bees. Social interaction time decreased by 43% for bees treated with a high sub-lethal dose of esfenvalerate. Bees exposed to a high sub-lethal dose of permethrin spent 67% less time in social interaction and spent more than 5 times as long in the food zone compared to control bees. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. 4DCAPTURE: a general purpose software package for capturing and analyzing two- and three-dimensional motion data acquired from video sequences

    Science.gov (United States)

    Walton, James S.; Hodgson, Peter; Hallamasek, Karen; Palmer, Jake

    2003-07-01

    4DVideo is creating a general purpose capability for capturing and analyzing kinematic data from video sequences in near real-time. The core element of this capability is a software package designed for the PC platform. The software ("4DCapture") is designed to capture and manipulate customized AVI files that can contain a variety of synchronized data streams -- including audio, video, centroid locations -- and signals acquired from more traditional sources (such as accelerometers and strain gauges.) The code includes simultaneous capture or playback of multiple video streams, and linear editing of the images (together with the ancilliary data embedded in the files). Corresponding landmarks seen from two or more views are matched automatically, and photogrammetric algorithms permit multiple landmarks to be tracked in two- and three-dimensions -- with or without lens calibrations. Trajectory data can be processed within the main application or they can be exported to a spreadsheet where they can be processed or passed along to a more sophisticated, stand-alone, data analysis application. Previous attempts to develop such applications for high-speed imaging have been limited in their scope, or by the complexity of the application itself. 4DVideo has devised a friendly ("FlowStack") user interface that assists the end-user to capture and treat image sequences in a natural progression. 4DCapture employs the AVI 2.0 standard and DirectX technology which effectively eliminates the file size limitations found in older applications. In early tests, 4DVideo has streamed three RS-170 video sources to disk for more than an hour without loss of data. At this time, the software can acquire video sequences in three ways: (1) directly, from up to three hard-wired cameras supplying RS-170 (monochrome) signals; (2) directly, from a single camera or video recorder supplying an NTSC (color) signal; and (3) by importing existing video streams in the AVI 1.0 or AVI 2.0 formats. The

  19. Diurnal variations in tear film break-up time determined in healthy subjects by software-assisted interpretation of tear film video recordings.

    Science.gov (United States)

    Pena-Verdeal, Hugo; García-Resúa, Carlos; Ramos, Lucía; Yebra-Pimentel, Eva; Giráldez, Ma Jesús

    2016-03-01

    This study was designed to examine diurnal variations in tear film break-up time (BUT) and maximum blink interval (MBI) and to assess two different ways of calculating these variables on video recordings of the BUT test interpreted with the help of especially designed software. The repeatability of interpreting BUT video recordings was also addressed. Twenty-six healthy young adults were enrolled after ruling out dry eye according to a battery of tests (ocular surface disease index, McMonnies questionnaire, Schirmer test, phenol red test and corneal staining). BUT and maximum blink interval were determined on video-recordings of the BUT test conducted over a day in four sessions (9.30 am, 12.30 pm, 3.30 pm and 6.30 pm). In each session, the test was repeated three times to give three videos in which three BUT and MBI values were obtained by a masked observer. BUT and MBI were determined by averaging the three measurements and by averaging only the two closest measurements. Finally, two further experienced observers re-examined the videos to assess the repeatability of the BUT measurements made. No diurnal variation in BUT was observed regardless of whether three or two video measurements were averaged. Significant correlation was detected between BUT and MBI. Inter-observer repeatability was better when BUT times were no longer than 15 seconds. Tear film BUT was not influenced by the time of day and moderate to strong correlation with MBI was observed in all four sessions. The software-assisted method proved useful and identified the need to clarify the BUT end-point and to limit the test to 15 seconds to improve observer repeatability. © 2016 Optometry Australia.

  20. Annotated Answer Set Programming

    OpenAIRE

    Straccia, Umberto

    2005-01-01

    We present Annotated Answer Set Programming, that extends the ex pressive power of disjunctive logic programming with annotation terms, taken from the generalized annotated logic programming framework.

  1. An integrated video-analysis software system designed for movement detection and sleep analysis. Validation of a tool for the behavioural study of sleep.

    Science.gov (United States)

    Scatena, Michele; Dittoni, Serena; Maviglia, Riccardo; Frusciante, Roberto; Testani, Elisa; Vollono, Catello; Losurdo, Anna; Colicchio, Salvatore; Gnoni, Valentina; Labriola, Claudio; Farina, Benedetto; Pennisi, Mariano Alberto; Della Marca, Giacomo

    2012-02-01

    The aim of the present study was to develop and validate a software tool for the detection of movements during sleep, based on the automated analysis of video recordings. This software is aimed to detect and quantify movements and to evaluate periods of sleep and wake. We applied an open-source software, previously distributed on the web (Zoneminder, ZM), meant for video surveillance. A validation study was performed: computed movement analysis was compared with two standardised, 'gold standard' methods for the analysis of sleep-wake cycles: actigraphy and laboratory-based video-polysomnography. Sleep variables evaluated by ZM were not different from those measured by traditional sleep-scoring systems. Bland-Altman plots showed an overlap between the scores obtained with ZM, PSG and actigraphy, with a slight tendency of ZM to overestimate nocturnal awakenings. ZM showed a good degree of accuracy both with respect to PSG (79.9%) and actigraphy (83.1%); and had very high sensitivity (ZM vs. PSG: 90.4%; ZM vs. actigraphy: 89.5%) and relatively lower specificity (ZM vs. PSG: 42.3%; ZM vs. actigraphy: 65.4%). The computer-assisted motion analysis is reliable and reproducible, and it can allow a reliable esteem of some sleep and wake parameters. The motion-based sleep analysis shows a trend to overestimate wakefulness. The possibility to measure sleep from video recordings may be useful in those clinical and experimental conditions in which traditional PSG studies may not be performed. Copyright © 2011 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  2. Feasibility of a cost-effective, video analysis software-based mobility protocol for objective spine kinematics and gait metrics: a proof of concept study.

    Science.gov (United States)

    Paul, Justin C; Petrizzo, Anthony; Rizzo, John-Ross; Bianco, Kristina; Maier, Stephen; Errico, Thomas J; Lafage, Virginie

    2015-03-01

    The purpose of this study was to investigate the potential of a high-throughput, easily implemented, cost-effective, video analysis software-based mobility protocol to quantify spine kinematics. This prospective cohort study of clinical biomechanics implemented 2-dimensional (2D) image processing at a tertiary-care academic institution. Ten healthy, able-bodied volunteers were recruited for 2D videography of gait and functional motion. The reliability of a 2D video analysis software program for gait and range of motion metrics was evaluated over 2 independent experimental sessions, assessing for inter-trial, inter-session, and inter-rater reliability. Healthy volunteers were evaluated for simple forward and side bending, rotation, treadmill stride length, and more complex seated-to-standing tasks. Based on established intraclass correlation coefficients, results indicated that reliability was considered good to excellent for simple forward and side bending, rotation, stride length, and more complex sit-to-standing tasks. In conclusion, a cost-effective, 2D, video analysis software-based mobility protocol represents a feasible and clinically useful approach for objective spine kinematics and gait metrics. As the complication rate of operative management in the setting of spinal deformity is weighed against functional performance and quality of life measures, an objective analysis tool in combination with an appropriate protocol will aid in clinical assessments and lead to an increased evidence base for management options and decision algorithms. Copyright © 2015 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  3. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

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

  5. DeTeCt 3.0: A software tool to detect impacts of small objects in video observations of Jupiter obtained by amateur astronomers

    Science.gov (United States)

    Juaristi, J.; Delcroix, M.; Hueso, R.; Sánchez-Lavega, A.

    2017-09-01

    Impacts of small size objects (10-20 m in diameter) with Jupiter atmosphere result in luminous superbolides that can be observed from the Earth with small size telescopes. Impacts of this kind have been observed four times by amateur astronomers since July 2010. The probability of observing one of these events is very small. Amateur astronomers observe Jupiter using fast video cameras that record thousands of frames during a few minutes which combine into a single image that generally results in a high-resolution image. Flashes are brief, faint and often lost by image reconstruction software. We present major upgrades in a software tool DeTeCt initially developed by amateur astronomer Marc Delcroix and our current project to maximize the chances of detecting more of these impacts in Jupiter.

  6. An Integrated Textbook, Video, and Software Environment for Novice and Expert Prolog Programmers. Technical Report No. 23.

    Science.gov (United States)

    Eisenstadt, Marc; Brayshaw, Mike

    This paper describes a Prolog execution model which serves as the uniform basis of textbook material, video-based teaching material, and an advanced graphical user interface for Prolog programmers. The model, based upon an augmented AND/OR tree representation of Prolog programs, uses an enriched "status box" in place of the traditional…

  7. Audiovisual heritage preservation in Earth and Space Science Informatics: Videos from Free and Open Source Software for Geospatial (FOSS4G) conferences in the TIB|AV-Portal.

    Science.gov (United States)

    Löwe, Peter; Marín Arraiza, Paloma; Plank, Margret

    2016-04-01

    The influence of Free and Open Source Software (FOSS) projects on Earth and Space Science Informatics (ESSI) continues to grow, particularly in the emerging context of Data Science or Open Science. The scientific significance and heritage of FOSS projects is only to a limited amount covered by traditional scientific journal articles: Audiovisual conference recordings contain significant information for analysis, reference and citation. In the context of data driven research, this audiovisual content needs to be accessible by effective search capabilities, enabling the content to be searched in depth and retrieved. Thereby, it is ensured that the content producers receive credit for their efforts within the respective communities. For Geoinformatics and ESSI, one distinguished driver is the OSGeo Foundation (OSGeo), founded in 2006 to support and promote the interdisciplinary collaborative development of open geospatial technologies and data. The organisational structure is based on software projects that have successfully passed the OSGeo incubation process, proving their compliance with FOSS licence models. This quality assurance is crucial for the transparent and unhindered application in (Open) Science. The main communication channels within and between the OSGeo-hosted community projects for face to face meetings are conferences on national, regional and global scale. Video recordings have been complementing the scientific proceedings since 2006. During the last decade, the growing body of OSGeo videos has been negatively affected by content loss, obsolescence of video technology and dependence on commercial video portals. Even worse, the distributed storage and lack of metadata do not guarantee concise and efficient access of the content. This limits the retrospective analysis of video content from past conferences. But, it also indicates a need for reliable, standardized, comparable audiovisual repositories for the future, as the number of OSGeo projects

  8. Debris in the deep: Using a 22-year video annotation database to survey marine litter in Monterey Canyon, central California, USA

    Science.gov (United States)

    Schlining, Kyra; von Thun, Susan; Kuhnz, Linda; Schlining, Brian; Lundsten, Lonny; Jacobsen Stout, Nancy; Chaney, Lori; Connor, Judith

    2013-09-01

    Anthropogenic marine debris is an increasing concern because of its potential negative impacts on marine ecosystems. This is a global problem that will have lasting effects for many reasons, including: (1) the input of debris into marine environments is likely to continue (commensurate with population increase and globalization), (2) accumulation, and possibly retention, of debris will occur in specific areas due to hydrography and geomorphology, and (3) the most common types of debris observed to date will likely persist for centuries. Due to the technical challenges and prohibitive costs of conducting research in the deep sea, little is known about the abundance, types, sources, and impacts of human refuse on this vast habitat, and the extreme depths to which this debris is penetrating has only recently been exposed. We reviewed 1149 video records of marine debris from 22 years of remotely operated vehicle deployments in Monterey Bay, covering depths from 25 m to 3971 m. We characterize debris by type, examine patterns of distribution, and discuss potential sources and dispersal mechanisms. Debris was most abundant within Monterey Canyon where aggregation and downslope transport of debris from the continental shelf are enhanced by natural canyon dynamics. The majority of debris was plastic (33%) and metal (23%). The highest relative frequencies of plastic and metal observations occurred below 2000 m, indicating that previous studies may greatly underestimate the extent of anthropogenic marine debris on the seafloor due to limitations in observing deeper regions. Our findings provide evidence that submarine canyons function to collect debris and act as conduits for debris transport from coastal to deep-sea habitats.

  9. Personalized video summarization based on group scoring

    OpenAIRE

    Darabi, K; G. Ghinea

    2014-01-01

    In this paper an expert-based model for generation of personalized video summaries is suggested. The video frames are initially scored and annotated by multiple video experts. Thereafter, the scores for the video segments that have been assigned the higher priorities by end users will be upgraded. Considering the required summary length, the highest scored video frames will be inserted into a personalized final summary. For evaluation purposes, the video summaries generated by our system have...

  10. Developing a Promotional Video

    Science.gov (United States)

    Epley, Hannah K.

    2014-01-01

    There is a need for Extension professionals to show clientele the benefits of their program. This article shares how promotional videos are one way of reaching audiences online. An example is given on how a promotional video has been used and developed using iMovie software. Tips are offered for how professionals can create a promotional video and…

  11. Three-dimensional image reconstruction with free open-source OsiriX software in video-assisted thoracoscopic lobectomy and segmentectomy.

    Science.gov (United States)

    Yao, Fei; Wang, Jian; Yao, Ju; Hang, Fangrong; Lei, Xu; Cao, Yongke

    2017-03-01

    The aim of this retrospective study was to evaluate the practice and the feasibility of Osirix, a free and open-source medical imaging software, in performing accurate video-assisted thoracoscopic lobectomy and segmentectomy. From July 2014 to April 2016, 63 patients received anatomical video-assisted thoracoscopic surgery (VATS), either lobectomy or segmentectomy, in our department. Three-dimensional (3D) reconstruction images of 61 (96.8%) patients were preoperatively obtained with contrast-enhanced computed tomography (CT). Preoperative resection simulations were accomplished with patient-individual reconstructed 3D images. For lobectomy, pulmonary lobar veins, arteries and bronchi were identified meticulously by carefully reviewing the 3D images on the display. For segmentectomy, the intrasegmental veins in the affected segment for division and the intersegmental veins to be preserved were identified on the 3D images. Patient preoperative characteristics, surgical outcomes and postoperative data were reviewed from a prospective database. The study cohort of 63 patients included 33 (52.4%) men and 30 (47.6%) women, of whom 46 (73.0%) underwent VATS lobectomy and 17 (27.0%) underwent VATS segmentectomy. There was 1 conversion from VATS lobectomy to open thoracotomy because of fibrocalcified lymph nodes. A VATS lobectomy was performed in 1 case after completing the segmentectomy because invasive adenocarcinoma was detected by intraoperative frozen-section analysis. There were no 30-day or 90-day operative mortalities CONCLUSIONS: The free, simple, and user-friendly software program Osirix can provide a 3D anatomic structure of pulmonary vessels and a clear vision into the space between the lesion and adjacent tissues, which allows surgeons to make preoperative simulations and improve the accuracy and safety of actual surgery. Copyright © 2017 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

  12. ANNOTATION SUPPORTED OCCLUDED OBJECT TRACKING

    Directory of Open Access Journals (Sweden)

    Devinder Kumar

    2012-08-01

    Full Text Available Tracking occluded objects at different depths has become as extremely important component of study for any video sequence having wide applications in object tracking, scene recognition, coding, editing the videos and mosaicking. The paper studies the ability of annotation to track the occluded object based on pyramids with variation in depth further establishing a threshold at which the ability of the system to track the occluded object fails. Image annotation is applied on 3 similar video sequences varying in depth. In the experiment, one bike occludes the other at a depth of 60cm, 80cm and 100cm respectively. Another experiment is performed on tracking humans with similar depth to authenticate the results. The paper also computes the frame by frame error incurred by the system, supported by detailed simulations. This system can be effectively used to analyze the error in motion tracking and further correcting the error leading to flawless tracking. This can be of great interest to computer scientists while designing surveillance systems etc.

  13. Android Video Streaming

    Science.gov (United States)

    2014-05-01

    be processed by a nearby high -performance computing asset and returned to a squad of Soldiers with annotations indicating the location of friendly and...is to change the resolution, bitrate, and/or framerate of the video being transmitted to the client, reducing the bandwidth requirements of the...video. This solution is typically not viable because a progressive download is required to have a constant resolution, bitrate, and framerate because

  14. Alignment-Annotator web server: rendering and annotating sequence alignments.

    Science.gov (United States)

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Video library for video imaging detection at intersection stop lines.

    Science.gov (United States)

    2010-04-01

    The objective of this activity was to record video that could be used for controlled : evaluation of video image vehicle detection system (VIVDS) products and software upgrades to : existing products based on a list of conditions that might be diffic...

  16. Revisiting the video stethoscope: an application of digital signal processing software (Goldwave) to monitoring ventilation in intubated patients.

    Science.gov (United States)

    Doyle, D John; Nair, Bala

    2009-01-01

    Problems with tracheal intubation and mechanical ventilation are potentially important causes of perioperative morbidity and mortality. We have developed a method of monitoring the ventilation of both lungs during general anesthesia that is an advanced digital version of a more primitive analog technique developed over two decades ago. We used two miniature electret microphones connected to regular chest pieces, placing the assemblies on the anterior chest wall about 4 inches below the clavicle in the midclavicular line. After amplification and 16-bit analog-to-digital conversion, the digital signal processing software package Goldwave (Version 5.12, www.goldwave. com) was used to produce real-time X-Y plots of the signals, with sounds from the right side plotted on the horizontal axis and sounds from the left side plotted on the vertical axis. Recognizing that when two signals are identical, their X-Y plot should form a 45 degree line, we hypothesized that X-Y plots obtained under endobronchial conditions would be recognizably different to plots reflecting normal bilateral lung ventilation. We also hypothesized that as a result of noise and anatomical variations that under conditions of bilateral mechanical ventilation the obtained plot would be very different from a simple 45 degree line. The data obtained supports these hypotheses. This preliminary study suggests that our technique may help provide a practical real-time warning system for detecting endotracheal tube malpositions, and may help build on the work of other investigators.

  17. Gamifying Video Object Segmentation.

    Science.gov (United States)

    Spampinato, Concetto; Palazzo, Simone; Giordano, Daniela

    2017-10-01

    Video object segmentation can be considered as one of the most challenging computer vision problems. Indeed, so far, no existing solution is able to effectively deal with the peculiarities of real-world videos, especially in cases of articulated motion and object occlusions; limitations that appear more evident when we compare the performance of automated methods with the human one. However, manually segmenting objects in videos is largely impractical as it requires a lot of time and concentration. To address this problem, in this paper we propose an interactive video object segmentation method, which exploits, on one hand, the capability of humans to identify correctly objects in visual scenes, and on the other hand, the collective human brainpower to solve challenging and large-scale tasks. In particular, our method relies on a game with a purpose to collect human inputs on object locations, followed by an accurate segmentation phase achieved by optimizing an energy function encoding spatial and temporal constraints between object regions as well as human-provided location priors. Performance analysis carried out on complex video benchmarks, and exploiting data provided by over 60 users, demonstrated that our method shows a better trade-off between annotation times and segmentation accuracy than interactive video annotation and automated video object segmentation approaches.

  18. Mining Crowdsourced First Impressions in Online Social Video

    OpenAIRE

    Biel, Joan-Isaac; Gatica-Perez, Daniel

    2014-01-01

    While multimedia and social computing research have used crowdsourcing techniques to annotate objects, actions, and scenes in social video sites like YouTube, little work has ad- dressed the crowdsourcing of personal and social traits in online social video or social media content in general. In this paper, we address the problems of (1) crowdsourcing the annotation of first impressions of video bloggers (vloggers) personal and social traits in conversational YouTube videos, and (2) mining th...

  19. Ubiquitous Annotation Systems

    DEFF Research Database (Denmark)

    Hansen, Frank Allan

    2006-01-01

    Ubiquitous annotation systems allow users to annotate physical places, objects, and persons with digital information. Especially in the field of location based information systems much work has been done to implement adaptive and context-aware systems, but few efforts have focused on the general...... requirements for linking information to objects in both physical and digital space. This paper surveys annotation techniques from open hypermedia systems, Web based annotation systems, and mobile and augmented reality systems to illustrate different approaches to four central challenges ubiquitous annotation...

  20. Teaching and Learning Communities through Online Annotation

    Science.gov (United States)

    van der Pluijm, B.

    2016-12-01

    during lecture presentation. Sharing of experiences and practices of annotation could benefit teachers and learners alike, and does not require complicated software, coding skills or special hardware environments.

  1. Stop-Frame Removal Improves Web Video Classification

    NARCIS (Netherlands)

    Habibian, A.; Snoek, C.G.M.

    2014-01-01

    Web videos available in sharing sites like YouTube, are becoming an alternative to manually annotated training data, which are necessary for creating video classifiers. However, when looking into web videos, we observe they contain several irrelevant frames that may randomly appear in any video,

  2. Interactive video algorithms and technologies

    CERN Document Server

    Hammoud, Riad

    2006-01-01

    This book covers both algorithms and technologies of interactive videos, so that businesses in IT and data managements, scientists and software engineers in video processing and computer vision, coaches and instructors that use video technology in teaching, and finally end-users will greatly benefit from it. This book contains excellent scientific contributions made by a number of pioneering scientists and experts from around the globe. It consists of five parts. The first part introduces the reader to interactive video and video summarization and presents effective methodologies for automatic abstraction of a single video sequence, a set of video sequences, and a combined audio-video sequence. In the second part, a list of advanced algorithms and methodologies for automatic and semi-automatic analysis and editing of audio-video documents are presented. The third part tackles a more challenging level of automatic video re-structuring, filtering of video stream by extracting of highlights, events, and meaningf...

  3. Reviews in instructional video

    NARCIS (Netherlands)

    van der Meij, Hans

    2017-01-01

    This study investigates the effectiveness of a video tutorial for software training whose construction was based on a combination of insights from multimedia learning and Demonstration-Based Training. In the videos, a model of task performance was enhanced with instructional features that were

  4. Digital Video Editing

    Science.gov (United States)

    McConnell, Terry

    2004-01-01

    Monica Adams, head librarian at Robinson Secondary in Fairfax country, Virginia, states that librarians should have the technical knowledge to support projects related to digital video editing. The process of digital video editing and the cables, storage issues and the computer system with software is described.

  5. Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

    Science.gov (United States)

    Pérez, Serge; Tubiana, Thibault; Imberty, Anne; Baaden, Marc

    2015-05-01

    A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e

  6. Studi Kualitas Video Streaming Dengan Menggunakan Flexipacket Radio

    OpenAIRE

    Fadly, Auliya

    2014-01-01

    Saat ini sistem komunikasi dengan mengunakan Video Streaming seringkali menjadi alternatif dalam berkomunikasi. Salah satu software pilihan untuk layananan Video Streaming adalah Windows Media Encoder yang dapat dimanfaatkan sebagai software server dan software VLC (VIdeoLAN Client) yang dapat dimanfaatkan sebagai software Client Video Streaming. Terdapat beberapa format Video Streaming yang tersedia di layanan internet seperti FLV, Mp4, AVI dan lain-lain. Pada Tugas Akhir ini dilakukan an...

  7. Video Analysis of Rolling Cylinders

    Science.gov (United States)

    Phommarach, S.; Wattanakasiwich, P.; Johnston, I.

    2012-01-01

    In this work, we studied the rolling motion of solid and hollow cylinders down an inclined plane at different angles. The motions were captured on video at 300 frames s[superscript -1], and the videos were analyzed frame by frame using video analysis software. Data from the real motion were compared with the theory of rolling down an inclined…

  8. JAABA: interactive machine learning for automatic annotation of animal behavior.

    Science.gov (United States)

    Kabra, Mayank; Robie, Alice A; Rivera-Alba, Marta; Branson, Steven; Branson, Kristin

    2013-01-01

    We present a machine learning-based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, including mice and adult and larval Drosophila.

  9. Digital Ink: In-Class Annotation of PowerPoint Lectures

    Science.gov (United States)

    Johnson, Anne E.

    2008-01-01

    Digital ink is a tool that, in conjunction with Microsoft PowerPoint software, allows real-time freehand annotation of presentations. Annotation of slides during class encourages student engagement with the material and problems under discussion. Digital ink annotation is a technique suitable for teaching across many disciplines, but is especially…

  10. Omics data management and annotation.

    Science.gov (United States)

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter.

  11. Comparative Genome Annotation.

    Science.gov (United States)

    König, Stefanie; Romoth, Lars; Stanke, Mario

    2018-01-01

    Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation. The reviewed methods include classical approaches such as the alignment of protein sequences or protein profiles against the genome and comparative gene prediction methods that exploit a genome alignment to annotate a target genome. Newer approaches such as the simultaneous annotation of multiple genomes are also reviewed. We discuss how the methods depend on the phylogenetic placement of genomes, give advice on the choice of methods, and examine the consistency between gene structure annotations in an example. Further, we provide practical advice on genome annotation in general.

  12. How usability is visible in video games

    OpenAIRE

    Saari, M

    2017-01-01

    Abstract As video games have become have become more popular and as popular as music and movies, the need for more video game developers have increased also. But even though there are more people developing video games, there still exists usability issues in video games like also in general computer software. The purpose of the thesis is to find out how usa...

  13. Solar Tutorial and Annotation Resource (STAR)

    Science.gov (United States)

    Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

    2009-12-01

    We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven

  14. Designing Annotation Tools based on Properties of Annotation Problems

    NARCIS (Netherlands)

    Reidsma, Dennis; Jovanovic, N.; Hofs, D.H.W.

    The creation of richly annotated, extendable and reusable corpora of multimodal interactions is an expensive and time-consuming task. Support from tools to create annotations is indispensable. This paper argues that annotation tools should be focused on specific classes of annotation problems to

  15. Storytelling machines for video search

    NARCIS (Netherlands)

    Habibian, A.

    2016-01-01

    We study a fundamental question for developing storytelling machines: what vocabulary is suited for machines to tell the story of a video? We start by manually specifying the vocabulary concepts and their annotations. In order to effectively handcraft the vocabulary, we empirically study what are

  16. Video Salient Object Detection via Fully Convolutional Networks.

    Science.gov (United States)

    Wang, Wenguan; Shen, Jianbing; Shao, Ling

    This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further

  17. Avoidable Software Procurements

    Science.gov (United States)

    2012-09-01

    basic functioning of federal agencies. GSA Advantage is an online purchasing service created by the GSA organization. Its mission is to provide a...managing enterprise software. Agreement negotiations and retail contracting actions are performed by IT acquisition and contracting professionals...deploying CICO technology, commercial IT industry leaders, such as Amazon and Apple, have been loaning out software titles, albeit video titles, for

  18. Annotation-based enrichment of Digital Objects using open-source frameworks

    Directory of Open Access Journals (Sweden)

    Marcus Emmanuel Barnes

    2017-07-01

    Full Text Available The W3C Web Annotation Data Model, Protocol, and Vocabulary unify approaches to annotations across the web, enabling their aggregation, discovery and persistence over time. In addition, new javascript libraries provide the ability for users to annotate multi-format content. In this paper, we describe how we have leveraged these developments to provide annotation features alongside Islandora’s existing preservation, access, and management capabilities. We also discuss our experience developing with the Web Annotation Model as an open web architecture standard, as well as our approach to integrating mature external annotation libraries. The resulting software (the Web Annotation Utility Module for Islandora accommodates annotation across multiple formats. This solution can be used in various digital scholarship contexts.

  19. GSV Annotated Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

    2010-09-14

    The following annotated bibliography was developed as part of the geospatial algorithm verification and validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Verification and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following five topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models. Many other papers were studied during the course of the investigation including. The annotations for these articles can be found in the paper "On the verification and validation of geospatial image analysis algorithms".

  20. Injectors and Annotations

    Science.gov (United States)

    Filman, Robert E.

    2004-01-01

    In a previous paper, we presented the Object Infrastructure Framework. The goal of that system is to simplify the creation of distributed applications. The primary claim of that work is that non-functional 'ilities' could be achieved by controlling and manipulating the communications between components, thereby simplifying the development of distributed systems. A secondary element of that paper is to argue for extending the conventional distributed objects model in two important ways: 1) The ability to insert injectors (filters, wrappers) into the communication path between components; 2) The ability to annotate communications with additional information, and to propagate these annotations through an application. Here we express the descriptions of that paper.

  1. Annotating Coloured Petri Nets

    DEFF Research Database (Denmark)

    Lindstrøm, Bo; Wells, Lisa Marie

    2002-01-01

    -net. An example of such auxiliary information is a counter which is associated with a token to be able to do performance analysis. Modifying colour sets and arc inscriptions in a CP-net to support a specific use may lead to creation of several slightly different CP-nets – only to support the different uses...... a method which makes it possible to associate auxiliary information, called annotations, with tokens without modifying the colour sets of the CP-net. Annotations are pieces of information that are not essential for determining the behaviour of the system being modelled, but are rather added to support...

  2. Applying negative rule mining to improve genome annotation

    Directory of Open Access Journals (Sweden)

    Frishman Goar

    2007-07-01

    Full Text Available Abstract Background Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items. Results Almost all exceptions from strong negative association rules are connected to at least one wrong attribute in the feature combination making up the rule. The fraction of annotation features flagged by this approach as suspicious is strongly enriched in errors and constitutes about 0.6% of the whole body of the similarity-transferred annotation in the PEDANT genome database. Positive rule mining does not identify two thirds of these errors. The approach based on exceptions from negative rules is much more specific than positive rule mining, but its coverage is significantly lower. Conclusion Mining of both negative and positive association rules is a potent tool for finding significant trends in protein annotation and flagging doubtful features for further inspection.

  3. Annotated bibliography traceability

    NARCIS (Netherlands)

    Narain, G.

    2006-01-01

    This annotated bibliography contains summaries of articles and chapters of books, which are relevant to traceability. After each summary there is a part about the relevancy of the paper for the LEI project. The aim of the LEI-project is to gain insight in several aspects of traceability in order to

  4. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  5. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...

  6. Modeling loosely annotated images using both given and imagined annotations

    Science.gov (United States)

    Tang, Hong; Boujemaa, Nozha; Chen, Yunhao; Deng, Lei

    2011-12-01

    In this paper, we present an approach to learn latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: 1. ambiguous correspondences between visual features and annotated keywords; 2. incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning a topic model. In particular, some ``imagined'' keywords are poured into the incomplete annotation through measuring similarity between keywords in terms of their co-occurrence. Then, both given and imagined annotations are employed to learn probabilistic topic models for automatically annotating new images. We conduct experiments on two image databases (i.e., Corel and ESP) coupled with their loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods. The proposed method improves word-driven probability latent semantic analysis (PLSA-words) up to a comparable performance with the best discrete annotation method, while a merit of PLSA-words is still kept, i.e., a wider semantic range.

  7. The effectiveness of annotated (vs. non-annotated) digital pathology slides as a teaching tool during dermatology and pathology residencies.

    Science.gov (United States)

    Marsch, Amanda F; Espiritu, Baltazar; Groth, John; Hutchens, Kelli A

    2014-06-01

    With today's technology, paraffin-embedded, hematoxylin & eosin-stained pathology slides can be scanned to generate high quality virtual slides. Using proprietary software, digital images can also be annotated with arrows, circles and boxes to highlight certain diagnostic features. Previous studies assessing digital microscopy as a teaching tool did not involve the annotation of digital images. The objective of this study was to compare the effectiveness of annotated digital pathology slides versus non-annotated digital pathology slides as a teaching tool during dermatology and pathology residencies. A study group composed of 31 dermatology and pathology residents was asked to complete an online pre-quiz consisting of 20 multiple choice style questions, each associated with a static digital pathology image. After completion, participants were given access to an online tutorial composed of digitally annotated pathology slides and subsequently asked to complete a post-quiz. A control group of 12 residents completed a non-annotated version of the tutorial. Nearly all participants in the study group improved their quiz score, with an average improvement of 17%, versus only 3% (P = 0.005) in the control group. These results support the notion that annotated digital pathology slides are superior to non-annotated slides for the purpose of resident education. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Feedback Driven Annotation and Refactoring of Parallel Programs

    DEFF Research Database (Denmark)

    Larsen, Per

    This thesis combines programmer knowledge and feedback to improve modeling and optimization of software. The research is motivated by two observations. First, there is a great need for automatic analysis of software for embedded systems - to expose and model parallelism inherent in programs. Second......, some program properties are beyond reach of such analysis for theoretical and practical reasons - but can be described by programmers. Three aspects are explored. The first is annotation of the source code. Two annotations are introduced. These allow more accurate modeling of parallelism...

  9. Video microblogging

    DEFF Research Database (Denmark)

    Bornoe, Nis; Barkhuus, Louise

    2010-01-01

    Microblogging is a recently popular phenomenon and with the increasing trend for video cameras to be built into mobile phones, a new type of microblogging has entered the arena of electronic communication: video microblogging. In this study we examine video microblogging, which is the broadcasting...... of short videos. A series of semi-structured interviews offers an understanding of why and how video microblogging is used and what the users post and broadcast....

  10. Software licenses: Stay honest!

    CERN Multimedia

    Computer Security Team

    2012-01-01

    Do you recall our article about copyright violation in the last issue of the CERN Bulletin, “Music, videos and the risk for CERN”? Now let’s be more precise. “Violating copyright” not only means the illegal download of music and videos, it also applies to software packages and applications.   Users must respect proprietary rights in compliance with the CERN Computing Rules (OC5). Not having legitimately obtained a program or the required licenses to run that software is not a minor offense. It violates CERN rules and puts the Organization at risk! Vendors deserve credit and compensation. Therefore, make sure that you have the right to use their software. In other words, you have bought the software via legitimate channels and use a valid and honestly obtained license. This also applies to “Shareware” and software under open licenses, which might also come with a cost. Usually, only “Freeware” is complete...

  11. Video processing project

    CSIR Research Space (South Africa)

    Globisch, R

    2009-03-01

    Full Text Available Video processing source code for algorithms and tools used in software media pipelines (e.g. image scalers, colour converters, etc.) The currently available source code is written in C++ with their associated libraries and DirectShow- Filters....

  12. Representing videos in tangible products

    Science.gov (United States)

    Fageth, Reiner; Weiting, Ralf

    2014-03-01

    Videos can be taken with nearly every camera, digital point and shoot cameras, DSLRs as well as smartphones and more and more with so-called action cameras mounted on sports devices. The implementation of videos while generating QR codes and relevant pictures out of the video stream via a software implementation was contents in last years' paper. This year we present first data about what contents is displayed and how the users represent their videos in printed products, e.g. CEWE PHOTOBOOKS and greeting cards. We report the share of the different video formats used, the number of images extracted out of the video in order to represent the video, the positions in the book and different design strategies compared to regular books.

  13. GSV Annotated Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

    2011-06-14

    The following annotated bibliography was developed as part of the Geospatial Algorithm Veri cation and Validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Veri cation and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following ve topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models.

  14. Diverse Image Annotation

    KAUST Repository

    Wu, Baoyuan

    2017-11-09

    In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

  15. The Genome Reverse Compiler: an explorative annotation tool

    Directory of Open Access Journals (Sweden)

    Warren Andrew S

    2009-01-01

    Full Text Available Abstract Background As sequencing costs have decreased, whole genome sequencing has become a viable and integral part of biological laboratory research. However, the tools with which genes can be found and functionally characterized have not been readily adapted to be part of the everyday biological sciences toolkit. Most annotation pipelines remain as a service provided by large institutions or come as an unwieldy conglomerate of independent components, each requiring their own setup and maintenance. Results To address this issue we have created the Genome Reverse Compiler, an easy-to-use, open-source, automated annotation tool. The GRC is independent of third party software installs and only requires a Linux operating system. This stands in contrast to most annotation packages, which typically require installation of relational databases, sequence similarity software, and a number of other programming language modules. We provide details on the methodology used by GRC and evaluate its performance on several groups of prokaryotes using GRC's built in comparison module. Conclusion Traditionally, to perform whole genome annotation a user would either set up a pipeline or take advantage of an online service. With GRC the user need only provide the genome he or she wants to annotate and the function resource files to use. The result is high usability and a very minimal learning curve for the intended audience of life science researchers and bioinformaticians. We believe that the GRC fills a valuable niche in allowing users to perform explorative, whole-genome annotation.

  16. The Effect of Educational Software, Video Modelling and Group Discussion on Social-Skill Acquisition Among Students with Mild Intellectual Disabilities.

    Science.gov (United States)

    Hetzroni, Orit E; Banin, Irit

    2017-07-01

    People with intellectual and developmental disabilities (IDD) often demonstrate difficulties in social skills. The purpose of this study was to examine the effects of a comprehensive intervention program on the acquisition of social skills among students with mild IDD. Single subject multiple baseline design across situations was used for teaching five school-age children with mild IDD social skills embedded in school-based situations. Results demonstrate that the intervention program that included video modelling and games embedded with group discussions and simulations increased the level and use of adequate social behaviours within the school's natural environment. Results demonstrate the unique attribution of a comprehensive interactive program for acquisition and transfer of participants' social skills such as language pragmatics and social rules within the school environment. Group discussions and simulations were beneficial and enabled both group and personalized instruction through the unique application of the program designed for the study. © 2016 John Wiley & Sons Ltd.

  17. Video demystified

    CERN Document Server

    Jack, Keith

    2004-01-01

    This international bestseller and essential reference is the "bible" for digital video engineers and programmers worldwide. This is by far the most informative analog and digital video reference available, includes the hottest new trends and cutting-edge developments in the field. Video Demystified, Fourth Edition is a "one stop" reference guide for the various digital video technologies. The fourth edition is completely updated with all new chapters on MPEG-4, H.264, SDTV/HDTV, ATSC/DVB, and Streaming Video (Video over DSL, Ethernet, etc.), as well as discussions of the latest standards throughout. The accompanying CD-ROM is updated to include a unique set of video test files in the newest formats. *This essential reference is the "bible" for digital video engineers and programmers worldwide *Contains all new chapters on MPEG-4, H.264, SDTV/HDTV, ATSC/DVB, and Streaming Video *Completely revised with all the latest and most up-to-date industry standards.

  18. Distinguished Books. Notable Books of 2002; Best Books for Young Adults; Audiobooks for Young Adults; Quick Picks for Reluctant Young Adult Readers; Notable Children's Books; Notable Children's Videos; Notable Recordings for Children; Notable Software for Children; Bestsellers of 2002; Literary Prizes, 2002.

    Science.gov (United States)

    Maryles, Daisy; Riippa, Laurele; Ink, Gary

    2003-01-01

    Includes bibliographies of notable books of 2002, including fiction, nonfiction, and poetry; books for young adults, including fiction, nonfiction, audiobooks, and titles for reluctant readers; notable books for children; videos for children; children's recordings and software; bestsellers, fiction and nonfiction; paperback bestsellers; almanacs,…

  19. Distinguished Books. Notable Books of 2001; Best Books for Young Adults; Quick Picks for Reluctant Young Adult Readers; Audiobooks for Young Adults; Notable Children's Books; Notable Children's Videos; Notable Recordings for Children; Notable software and Web Sites for Children; Bestsellers of 2001; Literary Prizes, 2001.

    Science.gov (United States)

    Maryles, Daisy; Riippa, Laurele; Ink, Gary

    2002-01-01

    Presents bibliographies of notable books, best books for young adults, audiobooks for young adults, notable children's books, notable children's videos, notable recordings for children, and notable software and Web sites for children; discusses bestsellers; and lists literary prizes awarded in 2001. (LRW)

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

    Science.gov (United States)

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

    2007-10-11

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

  1. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty...

  2. Jannovar: a java library for exome annotation.

    Science.gov (United States)

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

  3. COGNATE: comparative gene annotation characterizer.

    Science.gov (United States)

    Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

    2017-07-17

    The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https

  4. AnnoTrack - a tracking system for genome annotation

    Directory of Open Access Journals (Sweden)

    Hubbard Tim

    2010-10-01

    Full Text Available Abstract Background As genome sequences are determined for increasing numbers of model organisms, demand has grown for better tools to facilitate unified genome annotation efforts by communities of biologists. Typically this process involves numerous experts from the field and the use of data from dispersed sources as evidence. This kind of collaborative annotation project requires specialized software solutions for efficient data tracking and processing. Results As part of the scale-up phase of the ENCODE project (Encyclopedia of DNA Elements, the aim of the GENCODE project is to produce a highly accurate evidence-based reference gene annotation for the human genome. The AnnoTrack software system was developed to aid this effort. It integrates data from multiple distributed sources, highlights conflicts and facilitates the quick identification, prioritisation and resolution of problems during the process of genome annotation. Conclusions AnnoTrack has been in use for the last year and has proven a very valuable tool for large-scale genome annotation. Designed to interface with standard bioinformatics components, such as DAS servers and Ensembl databases, it is easy to setup and configure for different genome projects. The source code is available at http://annotrack.sanger.ac.uk.

  5. AutoFACT: An Automatic Functional Annotation and Classification Tool

    Directory of Open Access Journals (Sweden)

    Lang B Franz

    2005-06-01

    Full Text Available Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1 analyzes nucleotide and protein sequence data; (2 determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3 assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4 generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm.

  6. Metagenomic gene annotation by a homology-independent approach

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  7. Immersive video

    Science.gov (United States)

    Moezzi, Saied; Katkere, Arun L.; Jain, Ramesh C.

    1996-03-01

    Interactive video and television viewers should have the power to control their viewing position. To make this a reality, we introduce the concept of Immersive Video, which employs computer vision and computer graphics technologies to provide remote users a sense of complete immersion when viewing an event. Immersive Video uses multiple videos of an event, captured from different perspectives, to generate a full 3D digital video of that event. That is accomplished by assimilating important information from each video stream into a comprehensive, dynamic, 3D model of the environment. Using this 3D digital video, interactive viewers can then move around the remote environment and observe the events taking place from any desired perspective. Our Immersive Video System currently provides interactive viewing and `walkthrus' of staged karate demonstrations, basketball games, dance performances, and typical campus scenes. In its full realization, Immersive Video will be a paradigm shift in visual communication which will revolutionize television and video media, and become an integral part of future telepresence and virtual reality systems.

  8. THE DIMENSIONS OF COMPOSITION ANNOTATION.

    Science.gov (United States)

    MCCOLLY, WILLIAM

    ENGLISH TEACHER ANNOTATIONS WERE STUDIED TO DETERMINE THE DIMENSIONS AND PROPERTIES OF THE ENTIRE SYSTEM FOR WRITING CORRECTIONS AND CRITICISMS ON COMPOSITIONS. FOUR SETS OF COMPOSITIONS WERE WRITTEN BY STUDENTS IN GRADES 9 THROUGH 13. TYPESCRIPTS OF THE COMPOSITIONS WERE ANNOTATED BY CLASSROOM ENGLISH TEACHERS. THEN, 32 ENGLISH TEACHERS JUDGED…

  9. Annotation in Digital Scholarly Editions

    NARCIS (Netherlands)

    Boot, P.; Haentjens Dekker, R.

    2016-01-01

    Annotation in digital scholarly editions (of historical documents, literary works, letters, etc.) has long been recognized as an important desideratum, but has also proven to be an elusive ideal. In so far as annotation functionality is available, it is usually developed for a single edition and

  10. Drug Education: An Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.

    This bibliography consists of a total of 215 entries dealing with drug education, including curriculum guides, and drawn from documents in the ERIC system. There are two sections, the first containing 130 annotated citations of documents and journal articles, and the second containing 85 citations of journal articles without annotations, but with…

  11. Mesotext. Framing and exploring annotations

    NARCIS (Netherlands)

    Boot, P.; Boot, P.; Stronks, E.

    2007-01-01

    From the introduction: Annotation is an important item on the wish list for digital scholarly tools. It is one of John Unsworth’s primitives of scholarship (Unsworth 2000). Especially in linguistics,a number of tools have been developed that facilitate the creation of annotations to source material

  12. Automated cell tracking and analysis in phase-contrast videos (iTrack4U: development of Java software based on combined mean-shift processes.

    Directory of Open Access Journals (Sweden)

    Fabrice P Cordelières

    Full Text Available Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.

  13. Automated cell tracking and analysis in phase-contrast videos (iTrack4U): development of Java software based on combined mean-shift processes.

    Science.gov (United States)

    Cordelières, Fabrice P; Petit, Valérie; Kumasaka, Mayuko; Debeir, Olivier; Letort, Véronique; Gallagher, Stuart J; Larue, Lionel

    2013-01-01

    Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells.

  14. Morphosyntactic annotation of CHILDES transcripts*

    Science.gov (United States)

    SAGAE, KENJI; DAVIS, ERIC; LAVIE, ALON; MACWHINNEY, BRIAN; WINTNER, SHULY

    2014-01-01

    Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database with grammatical relations in the form of labeled dependency structures. We have produced a corpus of over 18,800 utterances (approximately 65,000 words) with manually curated gold-standard grammatical relation annotations. Using this corpus, we have developed a highly accurate data-driven parser for the English CHILDES data, which we used to automatically annotate the remainder of the English section of CHILDES. We have also extended the parser to Spanish, and are currently working on supporting more languages. The parser and the manually and automatically annotated data are freely available for research purposes. PMID:20334720

  15. Bridging analog and digital video in the surgical setting.

    Science.gov (United States)

    Miron, Hagai; Blumenthal, Eytan Z

    2003-10-01

    Editing surgical videos requires a basic understanding of key technical issues, especially when transforming from analog to digital media. These issues include an understanding of compression-decompression (eg, MPEGs), generation quality loss, video formats, and compression ratios. We introduce basic terminology and concepts related to analog and digital video, emphasizing the process of converting analog video to digital files. The choice of hardware, software, and formats is discussed, including advantages and drawbacks. Last, we provide an inexpensive hardware-software solution.

  16. Video games

    OpenAIRE

    Kolář, Vojtěch

    2012-01-01

    This thesis is based on a detailed analysis of various topics related to the question of whether video games can be art. In the first place it analyzes the current academic discussion on this subject and confronts different opinions of both supporters and objectors of the idea, that video games can be a full-fledged art form. The second point of this paper is to analyze the properties, that are inherent to video games, in order to find the reason, why cultural elite considers video games as i...

  17. ParsEval: parallel comparison and analysis of gene structure annotations

    Directory of Open Access Journals (Sweden)

    Standage Daniel S

    2012-08-01

    Full Text Available Abstract Background Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model genomes typically undergo several cycles of re-annotation. In many cases, it is not only different versions of annotations that need to be compared but also different sources of annotation of the same genome, derived from distinct gene prediction workflows. Such comparisons are of interest to annotation providers, prediction software developers, and end-users, who all need to assess what is common and what is different among distinct annotation sources. We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations. ParsEval calculates several statistics that highlight the similarities and differences between the two sets of annotations provided. These statistics are presented in an aggregate summary report, with additional details provided as individual reports specific to non-overlapping, gene-model-centric genomic loci. Genome browser styled graphics embedded in these reports help visualize the genomic context of the annotations. Output from ParsEval is both easily read and parsed, enabling systematic identification of problematic gene models for subsequent focused analysis. Results ParsEval is capable of analyzing annotations for large eukaryotic genomes on typical desktop or laptop hardware. In comparison to existing methods, ParsEval exhibits a considerable performance improvement, both in terms of runtime and memory consumption. Reports from ParsEval can provide relevant biological insights into the gene structure annotations being compared. Conclusions Implemented in C, ParsEval provides the quickest and most feature-rich solution for genome annotation comparison to date. The source code is freely available (under an ISC license at http://parseval.sourceforge.net/.

  18. Classifying smoke in laparoscopic videos using SVM

    Directory of Open Access Journals (Sweden)

    Alshirbaji Tamer Abdulbaki

    2017-09-01

    Full Text Available Smoke in laparoscopic videos usually appears due to the use of electrocautery when cutting or coagulating tissues. Therefore, detecting smoke can be used for event-based annotation in laparoscopic surgeries by retrieving the events associated with the electrocauterization. Furthermore, smoke detection can also be used for automatic smoke removal. However, detecting smoke in laparoscopic video is a challenge because of the changeability of smoke patterns, the moving camera and the different lighting conditions. In this paper, we present a video-based smoke detection algorithm to detect smoke of different densities such as fog, low and high density in laparoscopic videos. The proposed method depends on extracting various visual features from the laparoscopic images and providing them to support vector machine (SVM classifier. Features are based on motion, colour and texture patterns of the smoke. We validated our algorithm using experimental evaluation on four laparoscopic cholecystectomy videos. These four videos were manually annotated by defining every frame as smoke or non-smoke frame. The algorithm was applied to the videos by using different feature combinations for classification. Experimental results show that the combination of all proposed features gives the best classification performance. The overall accuracy (i.e. correctly classified frames is around 84%, with the sensitivity (i.e. correctly detected smoke frames and the specificity (i.e. correctly detected non-smoke frames are 89% and 80%, respectively.

  19. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

  20. Video recording in movement disorders: practical issues.

    Science.gov (United States)

    Duker, Andrew P

    2013-10-01

    Video recording can provide a valuable and unique record of the physical examinations of patients with a movement disorder, capturing nuances of movement and supplementing the written medical record. In addition, video is an indispensable tool for education and research in movement disorders. Digital file recording and storage has largely replaced analog tape recording, increasing the ease of editing and storing video records. Practical issues to consider include hardware and software configurations, video format, the security and longevity of file storage, patient consent, and video protocols.

  1. A prototype to automate the video subsystem routing for the video distribution subsystem of Space Station Freedom

    Science.gov (United States)

    Betz, Jessie M. Bethly

    1993-12-01

    The Video Distribution Subsystem (VDS) for Space Station Freedom provides onboard video communications. The VDS includes three major functions: external video switching; internal video switching; and sync and control generation. The Video Subsystem Routing (VSR) is a part of the VDS Manager Computer Software Configuration Item (VSM/CSCI). The VSM/CSCI is the software which controls and monitors the VDS equipment. VSR activates, terminates, and modifies video services in response to Tier-1 commands to connect video sources to video destinations. VSR selects connection paths based on availability of resources and updates the video routing lookup tables. This project involves investigating the current methodology to automate the Video Subsystem Routing and developing and testing a prototype as 'proof of concept' for designers.

  2. Annotating smart environment sensor data for activity learning.

    Science.gov (United States)

    Szewcyzk, S; Dwan, K; Minor, B; Swedlove, B; Cook, D

    2009-01-01

    The pervasive sensing technologies found in smart homes offer unprecedented opportunities for providing health monitoring and assistance to individuals experiencing difficulties living independently at home. In order to monitor the functional health of smart home residents, we need to design technologies that recognize and track the activities that people perform at home. Machine learning techniques can perform this task, but the software algorithms rely upon large amounts of sample data that is correctly labeled with the corresponding activity. Labeling, or annotating, sensor data with the corresponding activity can be time consuming, may require input from the smart home resident, and is often inaccurate. Therefore, in this paper we investigate four alternative mechanisms for annotating sensor data with a corresponding activity label. We evaluate the alternative methods along the dimensions of annotation time, resident burden, and accuracy using sensor data collected in a real smart apartment.

  3. Use of Annotations for Component and Framework Interoperability

    Science.gov (United States)

    David, O.; Lloyd, W.; Carlson, J.; Leavesley, G. H.; Geter, F.

    2009-12-01

    The popular programming languages Java and C# provide annotations, a form of meta-data construct. Software frameworks for web integration, web services, database access, and unit testing now take advantage of annotations to reduce the complexity of APIs and the quantity of integration code between the application and framework infrastructure. Adopting annotation features in frameworks has been observed to lead to cleaner and leaner application code. The USDA Object Modeling System (OMS) version 3.0 fully embraces the annotation approach and additionally defines a meta-data standard for components and models. In version 3.0 framework/model integration previously accomplished using API calls is now achieved using descriptive annotations. This enables the framework to provide additional functionality non-invasively such as implicit multithreading, and auto-documenting capabilities while achieving a significant reduction in the size of the model source code. Using a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside of it. To study the effectiveness of an annotation based framework approach with other modeling frameworks, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A monthly water balance model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. In a next step, the PRMS model was implemented in OMS 3.0 and is currently being implemented for water supply forecasting in the

  4. Processing sequence annotation data using the Lua programming language.

    Science.gov (United States)

    Ueno, Yutaka; Arita, Masanori; Kumagai, Toshitaka; Asai, Kiyoshi

    2003-01-01

    The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts, i.e. the handling of data containers, symbolic reference to data, and a simple programming syntax. Upon importing a foreign file, the original data are first decomposed in the Lua language while maintaining the original data schema. The converted data are parsed by the Lua interpreter and the contents are stored in our data warehouse. Then, portions of annotations are selected and arranged into our catalog format to be depicted on the sequence map. Our sequence visualization program was successfully implemented, embedding the Lua language for processing of annotation data and layout script. The program is available at http://staff.aist.go.jp/yutaka.ueno/guppy/.

  5. Video Salient Object Detection via Fully Convolutional Networks

    Science.gov (United States)

    Wang, Wenguan; Shen, Jianbing; Shao, Ling

    2018-01-01

    This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: (1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data, and (2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image datasets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the DAVIS dataset (MAE of .06) and the FBMS dataset (MAE of .07), and do so with much improved speed (2fps with all steps).

  6. A software-based solution for research in space ethology.

    Science.gov (United States)

    Tafforin, Carole; Gerebtzoff, Dimitri

    2010-10-01

    In this paper we present details of new applications of a software-based system for human ethological investigations in space missions and analogous settings. The studies address astronauts' motor adaptation to microgravity during short-term stays and the crews' social behavior in isolation and confinement over extended time periods. The current working hypotheses are based on differences observed in multicultural and mixed-gender crews for future interplanetary missions. In our approach, we use The Observer XT computer application to facilitate the observation, description, and quantification of behavioral data collected in parabolic flights, isolation and confinement campaigns, and polar missions. We implemented video recording protocols based on a goal-directed orientation task and daily life activities. The software integrates several steps: project management, definition of a coding scheme, annotation of videos linked to external data, data selection, and analysis. Numerical outcomes are presented. We show differences in motor skills between male (resting: 22%) and female (flexing/stretching: 22%) subjects in parabolic flights. We did not observe significant differences in social behavior by nationality during the isolation and confinement campaign. Notable findings include cultural grouping (20% of place preferences) and gender-based individuality (15%) during wintering at the polar base. The Observer XT may be a valuable tool to synchronize behavioral events with video files and bring forth visual representations and statistical analysis. It will be used for the next interdisciplinary project on the Mars 500 experiment to study physical ability, psychological capabilities, and behavioral performance over a 520-d stay in a simulated ground-based environment.

  7. Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

    Directory of Open Access Journals (Sweden)

    Mayer Klaus FX

    2007-08-01

    Full Text Available Abstract Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. Conclusion This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.

  8. Video Podcasts

    DEFF Research Database (Denmark)

    Nortvig, Anne Mette; Sørensen, Birgitte Holm

    2016-01-01

    This project’s aim was to support and facilitate master’s students’ preparation and collaboration by making video podcasts of short lectures available on YouTube prior to students’ first face-to-face seminar. The empirical material stems from group interviews, from statistical data created through...... YouTube analytics and from surveys answered by students after the seminar. The project sought to explore how video podcasts support learning and reflection online and how students use and reflect on the integration of online activities in the videos. Findings showed that students engaged actively...

  9. Online scene change detection of multicast (MBone) video

    Science.gov (United States)

    Zhou, Wensheng; Shen, Ye; Vellaikal, Asha; Kuo, C.-C. Jay

    1998-10-01

    Many multimedia applications, such as multimedia data management systems and communication systems, require efficient representation of multimedia content. Thus semantic interpretation of video content has been a popular research area. Currently, most content-based video representation involves the segmentation of video based on key frames which are generated using scene change detection techniques as well as camera/object motion. Then, video features can be extracted from key frames. However most of such research performs off-line video processing in which the whole video scope is known as a priori which allows multiple scans of the stored video files during video processing. In comparison, relatively not much research has been done in the area of on-line video processing, which is crucial in video communication applications such as on-line collaboration, news broadcasts and so on. Our research investigates on-line real-time scene change detection of multicast video over the Internet. Our on-line processing system are designed to meet the requirements of real-time video multicasting over the Internet and to utilize the successful video parsing techniques available today. The proposed algorithms extract key frames from video bitstreams sent through the MBone network, and the extracted key frames are multicasted as annotations or metadata over a separate channel to assist in content filtering such as those anticipated to be in use by on-line filtering proxies in the Internet. The performance of the proposed algorithms are demonstrated and discussed in this paper.

  10. Still image and video compression with MATLAB

    CERN Document Server

    Thyagarajan, K

    2010-01-01

    This book describes the principles of image and video compression techniques and introduces current and popular compression standards, such as the MPEG series. Derivations of relevant compression algorithms are developed in an easy-to-follow fashion. Numerous examples are provided in each chapter to illustrate the concepts. The book includes complementary software written in MATLAB SIMULINK to give readers hands-on experience in using and applying various video compression methods. Readers can enhance the software by including their own algorithms.

  11. ThermalTracker Software

    Energy Technology Data Exchange (ETDEWEB)

    2016-08-10

    The software processes recorded thermal video and detects the flight tracks of birds and bats that passed through the camera's field of view. The output is a set of images that show complete flight tracks for any detections, with the direction of travel indicated and the thermal image of the animal delineated. A report of the descriptive features of each detected track is also output in the form of a comma-separated value text file.

  12. SmashCommunity: A metagenomic annotation and analysis tool

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Harrington, Eoghan D; Foerstner, Konrad U

    2010-01-01

    SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate...... the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. AVAILABILITY: SmashCommunity is freely available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de....

  13. AIRS Maps from Space Processing Software

    Science.gov (United States)

    Thompson, Charles K.; Licata, Stephen J.

    2012-01-01

    This software package processes Atmospheric Infrared Sounder (AIRS) Level 2 swath standard product geophysical parameters, and generates global, colorized, annotated maps. It automatically generates daily and multi-day averaged colorized and annotated maps of various AIRS Level 2 swath geophysical parameters. It also generates AIRS input data sets for Eyes on Earth, Puffer-sphere, and Magic Planet. This program is tailored to AIRS Level 2 data products. It re-projects data into 1/4-degree grids that can be combined and averaged for any number of days. The software scales and colorizes global grids utilizing AIRS-specific color tables, and annotates images with title and color bar. This software can be tailored for use with other swath data products for the purposes of visualization.

  14. Tech Tips: Using Video Management/ Analysis Technology in Qualitative Research

    Directory of Open Access Journals (Sweden)

    J.A. Spiers

    2004-03-01

    Full Text Available This article presents tips on how to use video in qualitative research. The author states that, though there many complex and powerful computer programs for working with video, the work done in qualitative research does not require those programs. For this work, simple editing software is sufficient. Also presented is an easy and efficient method of transcribing video clips.

  15. Tech Tips: Using Video Management/ Analysis Technology in Qualitative Research

    OpenAIRE

    J.A. Spiers

    2004-01-01

    This article presents tips on how to use video in qualitative research. The author states that, though there many complex and powerful computer programs for working with video, the work done in qualitative research does not require those programs. For this work, simple editing software is sufficient. Also presented is an easy and efficient method of transcribing video clips.

  16. Geoscience Videos and Their Role in Supporting Student Learning

    Science.gov (United States)

    Wiggen, Jennifer; McDonnell, David

    2017-01-01

    A series of short (5 to 7 minutes long) geoscience videos were created to support student learning in a flipped class setting for an introductory geology class at North Carolina State University. Videos were made using a stylus, tablet, microphone, and video editing software. Essentially, we narrate a slide, sketch a diagram, or explain a figure…

  17. Annotated Bibliography of Psychomotor Testing.

    Science.gov (United States)

    1987-03-01

    1,5,13,25,26,38,49,64,65 Block packing test : 1,25,26,47 Block Stringing Test : 6,46,47 C Cancellation Test : 15 Cannabidiol , effects of: 15 Card sort test : 5 Central...6-AI81 694 ANNOTATED 81BLIOGRRPHY OF PSYCHOMOTOR TESTING (U) / ANTHROPOLOGY RESEA C PROJECT INC YELLOW SPRINGS OH C ERVIN MRR 87 AAMRL-TR-87-819...8217 + ’!’.1W’. + ... .,P- -) AAMRL-TR-87-019 tno S 00 :21" ANNOTATED BIBLIOGRAPHY OF PSYCHOMOTOR TESTING CAY ERVIN ANTHROPOLOGY RESEARCH PROJECT INC

  18. Code Generation for Protocols from CPN models Annotated with Pragmatics

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    them tend to be verbose and cluttered. Our code generation approach consists of three main steps, starting from a CPN model that the modeller has annotated with a set of pragmatics that make the protocol structure and the control-flow explicit. The first step is to compute for the CPN model, a set...... modelling languages, MDE further has the advantage that models are amenable to model checking which allows key behavioural properties of the software design to be verified. The combination of formally verified models and automated code generation contributes to a high degree of assurance that the resulting...... software implementation satisfies the properties verified for the model. Coloured Petri Nets (CPNs) have been widely used to model and verify protocol software, but limited work exists on using CPN models of protocol software as a basis for automated code generation. In this report, we present an approach...

  19. Akademisk video

    DEFF Research Database (Denmark)

    Frølunde, Lisbeth

    2017-01-01

    Dette kapitel har fokus på metodiske problemstillinger, der opstår i forhold til at bruge (digital) video i forbindelse med forskningskommunikation, ikke mindst online. Video har længe været benyttet i forskningen til dataindsamling og forskningskommunikation. Med digitaliseringen og internettet er...... der dog opstået nye muligheder og udfordringer i forhold til at formidle og distribuere forskningsresultater til forskellige målgrupper via video. Samtidig er klassiske metodologiske problematikker som forskerens positionering i forhold til det undersøgte stadig aktuelle. Både klassiske og nye...... problemstillinger diskuteres i kapitlet, som rammesætter diskussionen ud fra forskellige positioneringsmuligheder: formidler, historiefortæller, eller dialogist. Disse positioner relaterer sig til genrer inden for ’akademisk video’. Afslutningsvis præsenteres en metodisk værktøjskasse med redskaber til planlægning...

  20. CDMS (Clinical Data Mining Software): a cytokinome data mining system for a predictive medicine of chronic inflammatory diseases

    National Research Council Canada - National Science Library

    Evangelista, D; Colonna, G; Miele, M; Cutugno, F; Castello, G; Desantis, S; Costantini, S

    2010-01-01

    .... We developed a Clinical Data Mining Software to collect cytokine profiles evaluated on healthy subjects and patients by multiplex immunoassays also annotated with their clinical and laboratory data...

  1. A methodology and implementation for annotating digital images for context-appropriate use in an academic health care environment.

    Science.gov (United States)

    Goede, Patricia A; Lauman, Jason R; Cochella, Christopher; Katzman, Gregory L; Morton, David A; Albertine, Kurt H

    2004-01-01

    Use of digital medical images has become common over the last several years, coincident with the release of inexpensive, mega-pixel quality digital cameras and the transition to digital radiology operation by hospitals. One problem that clinicians, medical educators, and basic scientists encounter when handling images is the difficulty of using business and graphic arts commercial-off-the-shelf (COTS) software in multicontext authoring and interactive teaching environments. The authors investigated and developed software-supported methodologies to help clinicians, medical educators, and basic scientists become more efficient and effective in their digital imaging environments. The software that the authors developed provides the ability to annotate images based on a multispecialty methodology for annotation and visual knowledge representation. This annotation methodology is designed by consensus, with contributions from the authors and physicians, medical educators, and basic scientists in the Departments of Radiology, Neurobiology and Anatomy, Dermatology, and Ophthalmology at the University of Utah. The annotation methodology functions as a foundation for creating, using, reusing, and extending dynamic annotations in a context-appropriate, interactive digital environment. The annotation methodology supports the authoring process as well as output and presentation mechanisms. The annotation methodology is the foundation for a Windows implementation that allows annotated elements to be represented as structured eXtensible Markup Language and stored separate from the image(s).

  2. Software Open Source, Software Gratis?

    OpenAIRE

    Rakhmawati, Nur Aini

    2006-01-01

    Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI), memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT) saat ini. Beberapa organisasi dan Perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu so...

  3. Video Analytics

    DEFF Research Database (Denmark)

    This book collects the papers presented at two workshops during the 23rd International Conference on Pattern Recognition (ICPR): the Third Workshop on Video Analytics for Audience Measurement (VAAM) and the Second International Workshop on Face and Facial Expression Recognition (FFER) from Real...... World Videos. The workshops were run on December 4, 2016, in Cancun in Mexico. The two workshops together received 13 papers. Each paper was then reviewed by at least two expert reviewers in the field. In all, 11 papers were accepted to be presented at the workshops. The topics covered in the papers...

  4. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  5. MSDAC Resource Library Annotated Bibliography.

    Science.gov (United States)

    Watson, Cristel; And Others

    This annotated bibliography lists books, films, filmstrips, recordings, and booklets on sex equity. Entries are arranged according to the following topics: career resources, curriculum resources, management, sex equity, sex roles, women's studies, student activities, and sex-fair fiction. Included in each entry are name of author, editor or…

  6. Bioinformatics for plant genome annotation

    NARCIS (Netherlands)

    Fiers, M.W.E.J.

    2006-01-01

    Large amounts of genome sequence data are available and much more will become available in the near future. A DNA sequence alone has, however, limited use. Genome annotation is required to assign biological interpretation to the DNA sequence. This thesis

  7. Annotated Bibliography on Humanistic Education

    Science.gov (United States)

    Ganung, Cynthia

    1975-01-01

    Part I of this annotated bibliography deals with books and articles on such topics as achievement motivation, process education, transactional analysis, discipline without punishment, role-playing, interpersonal skills, self-acceptance, moral education, self-awareness, values clarification, and non-verbal communication. Part II focuses on…

  8. Video surveillance system based on MPEG-4

    Science.gov (United States)

    Ge, Jing; Zhang, Guoping; Yang, Zongkai

    2008-03-01

    Multimedia technology and networks protocol are the basic technology of the video surveillance system. A network remote video surveillance system based on MPEG-4 video coding standards is designed and implemented in this paper. The advantages of the MPEG-4 are analyzed in detail in the surveillance field, and then the real-time protocol and real-time control protocol (RTP/RTCP) are chosen as the networks transmission protocol. The whole system includes video coding control module, playing back module, network transmission module and network receiver module The scheme of management, control and storage about video data are discussed. The DirectShow technology is used to playback video data. The transmission scheme of digital video processing in networks, RTP packaging of MPEG-4 video stream is discussed. The receiver scheme of video date and mechanism of buffer are discussed. The most of the functions are archived by software, except that the video coding control module is achieved by hardware. The experiment results show that it provides good video quality and has the real-time performance. This system can be applied into wide fields.

  9. Multiview video codec based on KTA techniques

    Science.gov (United States)

    Seo, Jungdong; Kim, Donghyun; Ryu, Seungchul; Sohn, Kwanghoon

    2011-03-01

    Multi-view video coding (MVC) is a video coding standard developed by MPEG and VCEG for multi-view video. It showed average PSNR gain of 1.5dB compared with view-independent coding by H.264/AVC. However, because resolutions of multi-view video are getting higher for more realistic 3D effect, high performance video codec is needed. MVC adopted hierarchical B-picture structure and inter-view prediction as core techniques. The hierarchical B-picture structure removes the temporal redundancy, and the inter-view prediction reduces the inter-view redundancy by compensated prediction from the reconstructed neighboring views. Nevertheless, MVC has inherent limitation in coding efficiency, because it is based on H.264/AVC. To overcome the limit, an enhanced video codec for multi-view video based on Key Technology Area (KTA) is proposed. KTA is a high efficiency video codec by Video Coding Expert Group (VCEG), and it was carried out for coding efficiency beyond H.264/AVC. The KTA software showed better coding gain than H.264/AVC by using additional coding techniques. The techniques and the inter-view prediction are implemented into the proposed codec, which showed high coding gain compared with the view-independent coding result by KTA. The results presents that the inter-view prediction can achieve higher efficiency in a multi-view video codec based on a high performance video codec such as HEVC.

  10. Video Analytics

    DEFF Research Database (Denmark)

    This book collects the papers presented at two workshops during the 23rd International Conference on Pattern Recognition (ICPR): the Third Workshop on Video Analytics for Audience Measurement (VAAM) and the Second International Workshop on Face and Facial Expression Recognition (FFER) from Real W...

  11. Software engineering

    CERN Document Server

    Sommerville, Ian

    2010-01-01

    The ninth edition of Software Engineering presents a broad perspective of software engineering, focusing on the processes and techniques fundamental to the creation of reliable, software systems. Increased coverage of agile methods and software reuse, along with coverage of 'traditional' plan-driven software engineering, gives readers the most up-to-date view of the field currently available. Practical case studies, a full set of easy-to-access supplements, and extensive web resources make teaching the course easier than ever.

  12. Annotating images by mining image search results

    NARCIS (Netherlands)

    Wang, X.J.; Zhang, L.; Li, X.; Ma, W.Y.

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search

  13. Alcohol Education Materials; An Annotated Bibliography.

    Science.gov (United States)

    Milgram, Gail Gleason

    This 873-item annotated bibliography cites books, pamphlets, leaflets, and other materials produced for education about alcohol from 1950 to May 1973. The major part of each annotation is a brief summary of the contents. The annotation also contains a statement of orientation or type of presentation and evaluative comments. Each item is classified…

  14. Comparison of genetic variants in matched samples using thesaurus annotation.

    Science.gov (United States)

    Konopka, Tomasz; Nijman, Sebastian M B

    2016-03-01

    Calling changes in DNA, e.g. as a result of somatic events in cancer, requires analysis of multiple matched sequenced samples. Events in low-mappability regions of the human genome are difficult to encode in variant call files and have been under-reported as a result. However, they can be described accurately through thesaurus annotation-a technique that links multiple genomic loci together to explicate a single variant. We here describe software and benchmarks for using thesaurus annotation to detect point changes in DNA from matched samples. In benchmarks on matched normal/tumor samples we show that the technique can recover between five and ten percent more true events than conventional approaches, while strictly limiting false discovery and being fully consistent with popular variant analysis workflows. We also demonstrate the utility of the approach for analysis of de novo mutations in parents/child families. Software performing thesaurus annotation is implemented in java; available in source code on github at GeneticThesaurus (https://github.com/tkonopka/GeneticThesaurus) and as an executable on sourceforge at geneticthesaurus (https://sourceforge.net/projects/geneticthesaurus). Mutation calling is implemented in an R package available on github at RGeneticThesaurus (https://github.com/tkonopka/RGeneticThesaurus). Supplementary data are available at Bioinformatics online. tomasz.konopka@ludwig.ox.ac.uk. © The Author 2015. Published by Oxford University Press.

  15. "Annotated Lectures": Student-Instructor Interaction in Large-Scale Global Education

    Directory of Open Access Journals (Sweden)

    Roger Diehl

    2009-10-01

    Full Text Available We describe an "Annotated Lectures" system, which will be used in a global virtual teaching and student collaboration event on embodied intelligence presented by the University of Zurich. The lectures will be broadcasted via video-conference to lecture halls of different universities around the globe. Among other collaboration features, an "Annotated Lectures" system will be implemented in a 3D collaborative virtual environment and used by the participating students to make annotations to the video-recorded lectures, which will be sent to and answered by their supervisors, and forwarded to the lecturers in an aggregated way. The "Annotated Lectures" system aims to overcome the issues of limited studentinstructor interaction in large-scale education, and to foster an intercultural and multidisciplinary discourse among students who review the lectures in a group. After presenting the concept of the "Annotated Lectures" system, we discuss a prototype version including a description of the technical components and its expected benefit for large-scale global education.

  16. Video Playback Modifications for a DSpace Repository

    Directory of Open Access Journals (Sweden)

    Keith Gilbertson

    2016-01-01

    Full Text Available This paper focuses on modifications to an institutional repository system using the open source DSpace software to support playback of digital videos embedded within item pages. The changes were made in response to the formation and quick startup of an event capture group within the library that was charged with creating and editing video recordings of library events and speakers. This paper specifically discusses the selection of video formats, changes to the visual theme of the repository to allow embedded playback and captioning support, and modifications and bug fixes to the file downloading subsystem to enable skip-ahead playback of videos via byte-range requests. This paper also describes workflows for transcoding videos in the required formats, creating captions, and depositing videos into the repository.

  17. Human Pose Estimation and Activity Recognition from Multi-View Videos

    DEFF Research Database (Denmark)

    Holte, Michael Boelstoft; Tran, Cuong; Trivedi, Mohan

    2012-01-01

    –computer interaction (HCI), assisted living, gesture-based interactive games, intelligent driver assistance systems, movies, 3D TV and animation, physical therapy, autonomous mental development, smart environments, sport motion analysis, video surveillance, and video annotation. Next, we review and categorize recent...

  18. Video Analytics

    DEFF Research Database (Denmark)

    This book collects the papers presented at two workshops during the 23rd International Conference on Pattern Recognition (ICPR): the Third Workshop on Video Analytics for Audience Measurement (VAAM) and the Second International Workshop on Face and Facial Expression Recognition (FFER) from Real...... include: re-identification, consumer behavior analysis, utilizing pupillary response for task difficulty measurement, logo detection, saliency prediction, classification of facial expressions, face recognition, face verification, age estimation, super-resolution, pose estimation, and pain recognition...

  19. Video Analytics

    DEFF Research Database (Denmark)

    include: re-identification, consumer behavior analysis, utilizing pupillary response for task difficulty measurement, logo detection, saliency prediction, classification of facial expressions, face recognition, face verification, age estimation, super-resolution, pose estimation, and pain recognition......This book collects the papers presented at two workshops during the 23rd International Conference on Pattern Recognition (ICPR): the Third Workshop on Video Analytics for Audience Measurement (VAAM) and the Second International Workshop on Face and Facial Expression Recognition (FFER) from Real...

  20. SOFTWARE OPEN SOURCE, SOFTWARE GRATIS?

    Directory of Open Access Journals (Sweden)

    Nur Aini Rakhmawati

    2006-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI, memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT saat ini. Beberapa organisasi dan perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu software open source benar, untuk itu perlu dikenalkan konsep software open source mulai dari sejarah, lisensi dan bagaimana cara memilih lisensi, serta pertimbangan dalam memilih software open source yang ada. Kata kunci :Lisensi, Open Source, HAKI

  1. Evaluating Hierarchical Structure in Music Annotations

    Directory of Open Access Journals (Sweden)

    Brian McFee

    2017-08-01

    Full Text Available Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR, it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for “flat” descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

  2. Evaluating Hierarchical Structure in Music Annotations

    Science.gov (United States)

    McFee, Brian; Nieto, Oriol; Farbood, Morwaread M.; Bello, Juan Pablo

    2017-01-01

    Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for “flat” descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement. PMID:28824514

  3. Evaluating Hierarchical Structure in Music Annotations.

    Science.gov (United States)

    McFee, Brian; Nieto, Oriol; Farbood, Morwaread M; Bello, Juan Pablo

    2017-01-01

    Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for "flat" descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

  4. Recommendations for recognizing video events by concept vocabularies

    Science.gov (United States)

    2014-06-01

    detectors using the human annotated training data from two publicly available resources : the TRECVID 2012 Semantic Indexing task [47,3] and the...complex events in video. Acknowledgments This research is supported by the STW STORY project, the Dutch national program COMMIT, and by the

  5. Software Metrics and Software Metrology

    CERN Document Server

    Abran, Alain

    2010-01-01

    Most of the software measures currently proposed to the industry bring few real benefits to either software managers or developers. This book looks at the classical metrology concepts from science and engineering, using them as criteria to propose an approach to analyze the design of current software measures and then design new software measures (illustrated with the design of a software measure that has been adopted as an ISO measurement standard). The book includes several case studies analyzing strengths and weaknesses of some of the software measures most often quoted. It is meant for sof

  6. Computational annotation of genes differentially expressed along olive fruit development

    Directory of Open Access Journals (Sweden)

    Martinelli Federico

    2009-10-01

    Full Text Available Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1, completed pit hardening (stage 2 and veraison (stage 3] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B, and 2 and 3 (libraries C and D. All sequenced clones (1,132 in total were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO: cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was

  7. Intraprocedural Dataflow Analysis for Software Product Lines

    DEFF Research Database (Denmark)

    Brabrand, Claus; Ribeiro, Márcio; Tolêdo, Társis

    2013-01-01

    Software product lines (SPLs) developed using annotative approaches such as conditional compilation come with an inherent risk of constructing erroneous products. For this reason, it is essential to be able to analyze such SPLs. However, as dataflow analysis techniques are not able to deal with SPLs...

  8. Software reliability

    CERN Document Server

    Bendell, A

    1986-01-01

    Software Reliability reviews some fundamental issues of software reliability as well as the techniques, models, and metrics used to predict the reliability of software. Topics covered include fault avoidance, fault removal, and fault tolerance, along with statistical methods for the objective assessment of predictive accuracy. Development cost models and life-cycle cost models are also discussed. This book is divided into eight sections and begins with a chapter on adaptive modeling used to predict software reliability, followed by a discussion on failure rate in software reliability growth mo

  9. SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

    Directory of Open Access Journals (Sweden)

    Patel Viren

    2010-09-01

    Full Text Available Abstract Background The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. Results SeqAnt (Sequence Annotator is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. Conclusion SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.

  10. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

    Science.gov (United States)

    Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard

    2009-05-01

    The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation.

  11. Computational algorithms to predict Gene Ontology annotations

    Science.gov (United States)

    2015-01-01

    Background Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biological experiments and interpret their results. Despite their importance, these sources of information have some known issues. They are incomplete, since biological knowledge is far from being definitive and it rapidly evolves, and some erroneous annotations may be present. Since the curation process of novel annotations is a costly procedure, both in economical and time terms, computational tools that can reliably predict likely annotations, and thus quicken the discovery of new gene annotations, are very useful. Methods We used a set of computational algorithms and weighting schemes to infer novel gene annotations from a set of known ones. We used the latent semantic analysis approach, implementing two popular algorithms (Latent Semantic Indexing and Probabilistic Latent Semantic Analysis) and propose a novel method, the Semantic IMproved Latent Semantic Analysis, which adds a clustering step on the set of considered genes. Furthermore, we propose the improvement of these algorithms by weighting the annotations in the input set. Results We tested our methods and their weighted variants on the Gene Ontology annotation sets of three model organism genes (Bos taurus, Danio rerio and Drosophila melanogaster ). The methods showed their ability in predicting novel gene annotations and the weighting procedures demonstrated to lead to a valuable improvement, although the obtained results vary according to the dimension of the input annotation set and the considered algorithm. Conclusions Out of the three considered methods, the Semantic IMproved Latent Semantic Analysis is the one that provides better results. In particular, when coupled with a proper

  12. TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

    Science.gov (United States)

    Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

    2012-01-01

    In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

  13. Automatic Association of Chats and Video Tracks for Activity Learning and Recognition in Aerial Video Surveillance

    Directory of Open Access Journals (Sweden)

    Riad I. Hammoud

    2014-10-01

    Full Text Available We describe two advanced video analysis techniques, including video-indexed by voice annotations (VIVA and multi-media indexing and explorer (MINER. VIVA utilizes analyst call-outs (ACOs in the form of chat messages (voice-to-text to associate labels with video target tracks, to designate spatial-temporal activity boundaries and to augment video tracking in challenging scenarios. Challenging scenarios include low-resolution sensors, moving targets and target trajectories obscured by natural and man-made clutter. MINER includes: (1 a fusion of graphical track and text data using probabilistic methods; (2 an activity pattern learning framework to support querying an index of activities of interest (AOIs and targets of interest (TOIs by movement type and geolocation; and (3 a user interface to support streaming multi-intelligence data processing. We also present an activity pattern learning framework that uses the multi-source associated data as training to index a large archive of full-motion videos (FMV. VIVA and MINER examples are demonstrated for wide aerial/overhead imagery over common data sets affording an improvement in tracking from video data alone, leading to 84% detection with modest misdetection/false alarm results due to the complexity of the scenario. The novel use of ACOs and chat Sensors 2014, 14 19844 messages in video tracking paves the way for user interaction, correction and preparation of situation awareness reports.

  14. AGOUTI: improving genome assembly and annotation using transcriptome data.

    Science.gov (United States)

    Zhang, Simo V; Zhuo, Luting; Hahn, Matthew W

    2016-07-19

    Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species. We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on both simulated and real datasets, we show that it is highly accurate and that it achieves greater accuracy and contiguity when compared with other existing methods. AGOUTI is a powerful and effective scaffolder and, unlike most scaffolders, is expected to be more effective in larger genomes because of the commensurate increase in intron length. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the number of gene models by hundreds or thousands. The software is available free of charge under the MIT license.

  15. Extending eScience Provenance with User-Submitted Semantic Annotations

    Science.gov (United States)

    Michaelis, J.; Zednik, S.; West, P.; Fox, P. A.; McGuinness, D. L.

    2010-12-01

    eScience based systems generate provenance of their data products, related to such things as: data processing, data collection conditions, expert evaluation, and data product quality. Recent advances in web-based technology offer users the possibility of making annotations to both data products and steps in accompanying provenance traces, thereby expanding the utility of such provenance for others. These contributing users may have varying backgrounds, ranging from system experts to outside domain experts to citizen scientists. Furthermore, such users may wish to make varying types of annotations - ranging from documenting the purpose of a provenance step to raising concerns about the quality of data dependencies. Semantic Web technologies allow for such kinds of rich annotations to be made to provenance through the use of ontology vocabularies for (i) organizing provenance, and (ii) organizing user/annotation classifications. Furthermore, through Linked Data practices, Semantic linkages may be made from provenance steps to external data of interest. A desire for Semantically-annotated provenance has been motivated by data management issues in the Mauna Loa Solar Observatory’s (MLSO) Advanced Coronal Observing System (ACOS). In ACOS, photomoeter-based readings are taken of solar activity and subsequently processed into final data products consumable by end users. At intermediate stages of ACOS processing, factors such as evaluations by human experts and weather conditions are logged, which could impact data product quality. If such factors are linked via user-submitted annotations to provenance, it could be significantly beneficial for other users. Likewise, the background of a user could impact the credibility of their annotations. For example, an annotation made by a citizen scientist describing the purpose of a provenance step may not be as reliable as a similar annotation made by an ACOS project member. For this work, we have developed a software package that

  16. Digital video technology - today and tomorrow: 11th office information technology conference

    Energy Technology Data Exchange (ETDEWEB)

    Liberman, J.

    1994-10-01

    Digital video is probably computing`s fastest moving technology today. Just three years ago, the zenith of digital video technology on the PC was the successful marriage of digital text and graphics with analog audio and video by means of expensive analog laser disc players and video overlay boards. The state of the art involves two different approaches to fully digital video on computers: hardware-assisted and software-only solutions.

  17. Design of wireless video transmission system based on STM32 microcontroller

    Science.gov (United States)

    Yang, Fan; Ma, Chunting; Li, Haoyi

    2017-03-01

    The design of a wireless video transmission system based on STM32, the system uses the STM32F103VET6 microprocessor as the core, through the video acquisition module collects video data, video data will be sent to the receiver through the wireless transmitting module, receiving data will be displayed on the LCD screen. The software design process of receiver and transmitter is introduced. The experiment proves that the system realizes wireless video transmission function.

  18. Software engineering

    CERN Document Server

    Sommerville, Ian

    2016-01-01

    For courses in computer science and software engineering The Fundamental Practice of Software Engineering Software Engineering introduces readers to the overwhelmingly important subject of software programming and development. In the past few years, computer systems have come to dominate not just our technological growth, but the foundations of our world's major industries. This text seeks to lay out the fundamental concepts of this huge and continually growing subject area in a clear and comprehensive manner. The Tenth Edition contains new information that highlights various technological updates of recent years, providing readers with highly relevant and current information. Sommerville's experience in system dependability and systems engineering guides the text through a traditional plan-based approach that incorporates some novel agile methods. The text strives to teach the innovators of tomorrow how to create software that will make our world a better, safer, and more advanced place to live.

  19. Mass casualty incident surveillance and monitoring using identity aware video analytics.

    Science.gov (United States)

    Yu, Xunyi; Ganz, Aura

    2010-01-01

    In this paper, we propose an identity aware video analytic system that can assist securing the perimeter of a mass casualty incident scene and generate identity annotated video records for forensics and training purposes. Establishing a secure incident scene perimeter and enforcing access control to different zones is a demanding task for current video surveillance systems which lack the ability to provide the identity of the target and its security clearance. Our system which combines active RFID sensors with video analytic tools recovers the identity of the target enabling the activation of suitable alert policies. The system also enables annotation of incident scene video with identity metadata, facilitating the incident response process reconstruction for forensics analysis and emergency response training.

  20. FARAO: the flexible all-round annotation organizer.

    Science.gov (United States)

    Hammarén, Rickard; Pal, Chandan; Bengtsson-Palme, Johan

    2016-12-01

    With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets. FARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/ CONTACT: johan.bengtsson-palme@microbiology.seSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.

    Science.gov (United States)

    Tanizawa, Yasuhiro; Fujisawa, Takatomo; Nakamura, Yasukazu

    2017-11-02

    We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future. The software is implemented in Python 3 and runs in both Python 2.7 and 3.4- on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/. Supplementary data are available at Bioinformatics online. yn@nig.ac.jp.

  2. On the Use of Issue Tracking Annotations for Improving Developer Activity Metrics

    Directory of Open Access Journals (Sweden)

    Andrew Meneely

    2010-01-01

    Full Text Available Understanding and measuring how teams of developers collaborate on software projects can provide valuable insight into the software development process. Currently, researchers and practitioners measure developer collaboration with social networks constructed from version control logs. Version control change logs, however, do not tell the whole story. The collaborative problem-solving process is also documented in the issue tracking systems that record solutions to failures, feature requests, or other development tasks. We propose two annotations to be used in issue tracking systems: solution originator and solution approver. We annotated which developers were originators or approvers of the solution to 602 issues from the OpenMRS healthcare system. We used these annotations to augment the version control logs and found 47 more contributors to the OpenMRS project than the original 40 found in the version control logs. Using social network analysis, we found that approvers are likely to score high in centrality and hierarchical clustering. Our results indicate that our two issue tracking annotations identify project collaborators that version control logs miss. Thus, issue tracking annotations are an improvement in developer activity metrics that strengthen the connection between what we can measure in the project development artifacts and the team's collaborative problem-solving process.

  3. NEI You Tube Videos: Amblyopia

    Medline Plus

    Full Text Available ... NEI YouTube Videos > NEI YouTube Videos: Amblyopia NEI YouTube Videos YouTube Videos Home Age-Related Macular Degeneration ... Retinopathy of Prematurity Science Spanish Videos Webinars NEI YouTube Videos: Amblyopia Embedded video for NEI YouTube Videos: ...

  4. NEI You Tube Videos: Amblyopia

    Medline Plus

    Full Text Available ... YouTube Videos > NEI YouTube Videos: Amblyopia NEI YouTube Videos YouTube Videos Home Age-Related Macular Degeneration Amblyopia ... of Prematurity Science Spanish Videos Webinars NEI YouTube Videos: Amblyopia Embedded video for NEI YouTube Videos: Amblyopia ...

  5. NEI You Tube Videos: Amblyopia

    Science.gov (United States)

    ... YouTube Videos > NEI YouTube Videos: Amblyopia NEI YouTube Videos YouTube Videos Home Age-Related Macular Degeneration Amblyopia ... of Prematurity Science Spanish Videos Webinars NEI YouTube Videos: Amblyopia Embedded video for NEI YouTube Videos: Amblyopia ...

  6. Stealthy annotation of experimental biology by spreadsheets.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Horridge, M.; Jupp, S.; Krebs, O.; Snoep, J.L.; du Preez, F.B.; Mueller, W.; Stevens, R.; Goble, C.A.

    2013-01-01

    The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in semantic data annotation and in the constriction of terminologies and ontologies used for annotation.

  7. Practical Linguistic Annotation : The Hebrew Bible

    NARCIS (Netherlands)

    Roorda, Dirk

    2017-01-01

    Annotation and research in the humanities are tightly coupled. Annotations can be seen as expressions of research activity which can be turned into input data for subsequent research. The digital paradigm has profoundly altered the ways in which we humans can handle the information content of our

  8. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  9. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis

    2015-01-01

    easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were evaluated running an inter-annotator reliability study on three different speech styles (read speech, monologue and dialogue...

  10. A Pilot Study on Developing a Standardized and Sensitive School Violence Risk Assessment with Manual Annotation.

    Science.gov (United States)

    Barzman, Drew H; Ni, Yizhao; Griffey, Marcus; Patel, Bianca; Warren, Ashaki; Latessa, Edward; Sorter, Michael

    2017-09-01

    School violence has increased over the past decade and innovative, sensitive, and standardized approaches to assess school violence risk are needed. In our current feasibility study, we initialized a standardized, sensitive, and rapid school violence risk approach with manual annotation. Manual annotation is the process of analyzing a student's transcribed interview to extract relevant information (e.g., key words) to school violence risk levels that are associated with students' behaviors, attitudes, feelings, use of technology (social media and video games), and other activities. In this feasibility study, we first implemented school violence risk assessments to evaluate risk levels by interviewing the student and parent separately at the school or the hospital to complete our novel school safety scales. We completed 25 risk assessments, resulting in 25 transcribed interviews of 12-18 year olds from 15 schools in Ohio and Kentucky. We then analyzed structured professional judgments, language, and patterns associated with school violence risk levels by using manual annotation and statistical methodology. To analyze the student interviews, we initiated the development of an annotation guideline to extract key information that is associated with students' behaviors, attitudes, feelings, use of technology and other activities. Statistical analysis was applied to associate the significant categories with students' risk levels to identify key factors which will help with developing action steps to reduce risk. In a future study, we plan to recruit more subjects in order to fully develop the manual annotation which will result in a more standardized and sensitive approach to school violence assessments.

  11. NLR-parser: rapid annotation of plant NLR complements.

    Science.gov (United States)

    Steuernagel, Burkhard; Jupe, Florian; Witek, Kamil; Jones, Jonathan D G; Wulff, Brande B H

    2015-05-15

    The repetitive nature of plant disease resistance genes encoding for nucleotide-binding leucine-rich repeat (NLR) proteins hampers their prediction with standard gene annotation software. Motif alignment and search tool (MAST) has previously been reported as a tool to support annotation of NLR-encoding genes. However, the decision if a motif combination represents an NLR protein was entirely manual. The NLR-parser pipeline is designed to use the MAST output from six-frame translated amino acid sequences and filters for predefined biologically curated motif compositions. Input reads can be derived from, for example, raw long-read sequencing data or contigs and scaffolds coming from plant genome projects. The output is a tab-separated file with information on start and frame of the first NLR specific motif, whether the identified sequence is a TNL or CNL, potentially full or fragmented. In addition, the output of the NB-ARC domain sequence can directly be used for phylogenetic analyses. In comparison to other prediction software, the highly complex NB-ARC domain is described in detail using several individual motifs. © The Author 2015. Published by Oxford University Press.

  12. A Benchmark Dataset and Saliency-guided Stacked Autoencoders for Video-based Salient Object Detection.

    Science.gov (United States)

    Li, Jia; Xia, Changqun; Chen, Xiaowu

    2017-10-12

    Image-based salient object detection (SOD) has been extensively studied in past decades. However, video-based SOD is much less explored due to the lack of large-scale video datasets within which salient objects are unambiguously defined and annotated. Toward this end, this paper proposes a video-based SOD dataset that consists of 200 videos. In constructing the dataset, we manually annotate all objects and regions over 7,650 uniformly sampled keyframes and collect the eye-tracking data of 23 subjects who free-view all videos. From the user data, we find that salient objects in a video can be defined as objects that consistently pop-out throughout the video, and objects with such attributes can be unambiguously annotated by combining manually annotated object/region masks with eye-tracking data of multiple subjects. To the best of our knowledge, it is currently the largest dataset for videobased salient object detection. Based on this dataset, this paper proposes an unsupervised baseline approach for video-based SOD by using saliencyguided stacked autoencoders. In the proposed approach, multiple spatiotemporal saliency cues are first extracted at the pixel, superpixel and object levels. With these saliency cues, stacked autoencoders are constructed in an unsupervised manner that automatically infers a saliency score for each pixel by progressively encoding the high-dimensional saliency cues gathered from the pixel and its spatiotemporal neighbors. In experiments, the proposed unsupervised approach is compared with 31 state-of-the-art models on the proposed dataset and outperforms 30 of them, including 19 imagebased classic (unsupervised or non-deep learning) models, six image-based deep learning models, and five video-based unsupervised models. Moreover, benchmarking results show that the proposed dataset is very challenging and has the potential to boost the development of video-based SOD.

  13. Educational Video Recording and Editing for The Hand Surgeon

    OpenAIRE

    Rehim, Shady A.; Chung, Kevin C.

    2015-01-01

    Digital video recordings are increasingly used across various medical and surgical disciplines including hand surgery for documentation of patient care, resident education, scientific presentations and publications. In recent years, the introduction of sophisticated computer hardware and software technology has simplified the process of digital video production and improved means of disseminating large digital data files. However, the creation of high quality surgical video footage requires b...

  14. Rheumatoid Arthritis Educational Video Series

    Medline Plus

    Full Text Available ... Rheumatoid Arthritis Educational Video Series Rheumatoid Arthritis Educational Video Series This series of five videos was designed ... Activity Role of Body Weight in Osteoarthritis Educational Videos for Patients Rheumatoid Arthritis Educational Video Series Psoriatic ...

  15. Software requirements

    CERN Document Server

    Wiegers, Karl E

    2003-01-01

    Without formal, verifiable software requirements-and an effective system for managing them-the programs that developers think they've agreed to build often will not be the same products their customers are expecting. In SOFTWARE REQUIREMENTS, Second Edition, requirements engineering authority Karl Wiegers amplifies the best practices presented in his original award-winning text?now a mainstay for anyone participating in the software development process. In this book, you'll discover effective techniques for managing the requirements engineering process all the way through the development cy

  16. High-Speed Video Analysis in a Conceptual Physics Class

    Science.gov (United States)

    Desbien, Dwain M.

    2011-01-01

    The use of probe ware and computers has become quite common in introductory physics classrooms. Video analysis is also becoming more popular and is available to a wide range of students through commercially available and/or free software. Video analysis allows for the study of motions that cannot be easily measured in the traditional lab setting…

  17. 61214++++','DOAJ-ART-EN'); return false;" href="+++++https://jual.nipissingu.ca/wp-content/uploads/sites/25/2014/06/v61214.m4v">61214++++">Jailed - Video

    Directory of Open Access Journals (Sweden)

    Cameron CULBERT

    2012-07-01

    Full Text Available As the public education system in Northern Ontario continues to take a downward spiral, a plethora of secondary school students are being placed in an alternative educational environment. Juxtaposing the two educational settings reveals very similar methods and characteristics of educating our youth as opposed to using a truly alternative approach to education. This video reviews the relationship between public education and alternative education in a remote Northern Ontario setting. It is my belief that the traditional methods of teaching are not appropriate in educating at risk students in alternative schools. Paper and pencil worksheets do not motivate these students to learn and succeed. Alternative education should emphasize experiential learning, a just in time curriculum based on every unique individual and the students true passion for everyday life. Cameron Culbert was born on February 3rd, 1977 in North Bay, Ontario. His teenage years were split between attending public school and his willed curriculum on the ski hill. Culbert spent 10 years (1996-2002 & 2006-2010 competing for Canada as an alpine ski racer. His passion for teaching and coaching began as an athlete and has now transferred into the classroom and the community. As a graduate of Nipissing University (BA, BEd, MEd. Camerons research interests are alternative education, physical education and technology in the classroom. Currently Cameron is an active educator and coach in Northern Ontario.

  18. Concept annotation in the CRAFT corpus

    Directory of Open Access Journals (Sweden)

    Bada Michael

    2012-07-01

    Full Text Available Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released. Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens, our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection, the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are

  19. Manual Annotation of Translational Equivalence The Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    Bilingual annotators were paid to link roughly sixteen thousand corresponding words between on-line versions of the Bible in modern French and modern English. These annotations are freely available to the research community from http://www.cis.upenn.edu/~melamed . The annotations can be used for several purposes. First, they can be used as a standard data set for developing and testing translation lexicons and statistical translation models. Second, researchers in lexical semantics will be able to mine the annotations for insights about cross-linguistic lexicalization patterns. Third, the annotations can be used in research into certain recently proposed methods for monolingual word-sense disambiguation. This paper describes the annotated texts, the specially-designed annotation tool, and the strategies employed to increase the consistency of the annotations. The annotation process was repeated five times by different annotators. Inter-annotator agreement rates indicate that the annotations are reasonably rel...

  20. Interoperable Multimedia Annotation and Retrieval for the Tourism Sector

    NARCIS (Netherlands)

    Chatzitoulousis, Antonios; Efraimidis, Pavlos S.; Athanasiadis, I.N.

    2015-01-01

    The Atlas Metadata System (AMS) employs semantic web annotation techniques in order to create an interoperable information annotation and retrieval platform for the tourism sector. AMS adopts state-of-the-art metadata vocabularies, annotation techniques and semantic web technologies.

  1. Video Design Games

    DEFF Research Database (Denmark)

    Smith, Rachel Charlotte; Christensen, Kasper Skov; Iversen, Ole Sejer

    We introduce Video Design Games to train educators in teaching design. The Video Design Game is a workshop format consisting of three rounds in which participants observe, reflect and generalize based on video snippets from their own practice. The paper reports on a Video Design Game workshop...

  2. Software Innovation

    DEFF Research Database (Denmark)

    Rose, Jeremy

      Innovation is the forgotten key to modern systems development - the element that defines the enterprising engineer, the thriving software firm and the cutting edge software application.  Traditional forms of technical education pay little attention to creativity - often encouraging overly...... rationalistic ways of thinking which stifle the ability to innovate. Professional software developers are often drowned in commercial drudgery and overwhelmed by work pressure and deadlines. The topic that will both ensure success in the market and revitalize their work lives is never addressed. This book sets...... out the new field of software innovation. It organizes the existing scientific research into eight simple heuristics - guiding principles for organizing a system developer's work-life so that it focuses on innovation....

  3. Characterization of social video

    Science.gov (United States)

    Ostrowski, Jeffrey R.; Sarhan, Nabil J.

    2009-01-01

    The popularity of social media has grown dramatically over the World Wide Web. In this paper, we analyze the video popularity distribution of well-known social video websites (YouTube, Google Video, and the AOL Truveo Video Search engine) and characterize their workload. We identify trends in the categories, lengths, and formats of those videos, as well as characterize the evolution of those videos over time. We further provide an extensive analysis and comparison of video content amongst the main regions of the world.

  4. Automatic blood detection in capsule endoscopy video

    Science.gov (United States)

    Novozámský, Adam; Flusser, Jan; Tachecí, Ilja; Sulík, Lukáš; Bureš, Jan; Krejcar, Ondřej

    2016-12-01

    We propose two automatic methods for detecting bleeding in wireless capsule endoscopy videos of the small intestine. The first one uses solely the color information, whereas the second one incorporates the assumptions about the blood spot shape and size. The original idea is namely the definition of a new color space that provides good separability of blood pixels and intestinal wall. Both methods can be applied either individually or their results can be fused together for the final decision. We evaluate their individual performance and various fusion rules on real data, manually annotated by an endoscopist.

  5. Video visual analytics

    OpenAIRE

    Höferlin, Markus Johannes

    2013-01-01

    The amount of video data recorded world-wide is tremendously growing and has already reached hardly manageable dimensions. It originates from a wide range of application areas, such as surveillance, sports analysis, scientific video analysis, surgery documentation, and entertainment, and its analysis represents one of the challenges in computer science. The vast amount of video data renders manual analysis by watching the video data impractical. However, automatic evaluation of video material...

  6. The Effects of Reviews in Video Tutorials

    Science.gov (United States)

    van der Meij, H.; van der Meij, J.

    2016-01-01

    This study investigates how well a video tutorial for software training that is based on Demonstration-Based Teaching supports user motivation and performance. In addition, it is studied whether reviews significantly contribute to these measures. The Control condition employs a tutorial with instructional features added to a dynamic task…

  7. The effects of reviews in video tutorials

    NARCIS (Netherlands)

    van der Meij, Hans; van der Meij, Jan

    2016-01-01

    This study investigates how well a video tutorial for software training that is based on Demonstration-Based Teaching supports user motivation and performance. In addition, it is studied whether reviews significantly contribute to these measures. The Control condition employs a tutorial with

  8. An Introduction to Recording, Editing, and Streaming Picture-in-Picture Ultrasound Videos.

    Science.gov (United States)

    Rajasekaran, Sathish; Hall, Mederic M; Finnoff, Jonathan T

    2016-08-01

    This paper describes the process by which high-definition resolution (up to 1920 × 1080 pixels) ultrasound video can be captured in conjunction with high-definition video of the transducer position (picture-in-picture). In addition, we describe how to edit the recorded video feeds to combine both feeds, and to crop, resize, split, stitch, cut, annotate videos, and also change the frame rate, insert pictures, edit the audio feed, and use chroma keying. We also describe how to stream a picture-in-picture ultrasound feed during a videoconference. Copyright © 2016 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  9. Spatial-temporal forensic analysis of mass casualty incidents using video sequences.

    Science.gov (United States)

    Hao Dong; Juechen Yin; Schafer, James; Ganz, Aura

    2016-08-01

    In this paper we introduce DIORAMA based forensic analysis of mass casualty incidents (MCI) using video sequences. The video sequences captured on site are automatically annotated by metadata, which includes the capture time and the camera location and viewing direction. Using a visual interface the MCI investigators can easily understand the availability of video clips in specific areas of interest, and efficiently review them. The video-based forensic analysis system will enable the MCI investigators to better understand the rescue operations and subsequently improve training procedures.

  10. An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets

    Directory of Open Access Journals (Sweden)

    Matthews Benjamin F

    2010-07-01

    Full Text Available Abstract Background The data produced by an Illumina flow cell with all eight lanes occupied, produces well over a terabyte worth of images with gigabytes of reads following sequence alignment. The ability to translate such reads into meaningful annotation is therefore of great concern and importance. Very easily, one can get flooded with such a great volume of textual, unannotated data irrespective of read quality or size. CASAVA, a optional analysis tool for Illumina sequencing experiments, enables the ability to understand INDEL detection, SNP information, and allele calling. To not only extract from such analysis, a measure of gene expression in the form of tag-counts, but furthermore to annotate such reads is therefore of significant value. Findings We developed TASE (Tag counting and Analysis of Solexa Experiments, a rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets. Developed in Java and deployed using jTDS JDBC driver and a SQL Server backend, TASE provides an extremely fast means of calculating gene expression through tag-counts while annotating sequenced reads with the gene's presumed function, from any given CASAVA-build. Such a build is generated for both DNA and RNA sequencing. Analysis is broken into two distinct components: DNA sequence or read concatenation, followed by tag-counting and annotation. The end result produces output containing the homology-based functional annotation and respective gene expression measure signifying how many times sequenced reads were found within the genomic ranges of functional annotations. Conclusions TASE is a powerful tool to facilitate the process of annotating a given Illumina Solexa sequencing dataset. Our results indicate that both homology-based annotation and tag-count analysis are achieved in very efficient times, providing researchers to delve deep in a given CASAVA-build and maximize information extraction from a sequencing

  11. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  12. Subjective Video Quality Assessment in H.264/AVC Video Coding Standard

    Directory of Open Access Journals (Sweden)

    Z. Miličević

    2012-11-01

    Full Text Available This paper seeks to provide an approach for subjective video quality assessment in the H.264/AVC standard. For this purpose a special software program for the subjective assessment of quality of all the tested video sequences is developed. It was developed in accordance with recommendation ITU-T P.910, since it is suitable for the testing of multimedia applications. The obtained results show that in the proposed selective intra prediction and optimized inter prediction algorithm there is a small difference in picture quality (signal-to-noise ratio between decoded original and modified video sequences.

  13. Annotation Style Guide for the Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    This annotation style guide was created by and for the Blinker project at the University of Pennsylvania. The Blinker project was so named after the ``bilingual linker'' GUI, which was created to enable bilingual annotators to ``link'' word tokens that are mutual translations in parallel texts. The parallel text chosen for this project was the Bible, because it is probably the easiest text to obtain in electronic form in multiple languages. The languages involved were English and French, because, of the languages with which the project co-ordinator was familiar, these were the two for which a sufficient number of annotators was likely to be found.

  14. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    ) language drift on Twitter is significant, and while off-the-shelf systems have been reported to perform well on in-sample data, they often perform poorly on new samples of tweets, (b) state-of-the-art performance across various datasets can beobtained from crowdsourced annotations, making it more feasible......We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a...

  15. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    2015-01-01

    , the user simply captures an image using the HMD’s camera, looks at an object of interest in the image, and speaks out the information to be associated with the object. The gaze location is recorded and visualized with a marker. The voice is transcribed using speech recognition. Gaze annotations can......To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion...

  16. Annotation of selection strengths in viral genomes

    DEFF Research Database (Denmark)

    McCauley, Stephen; de Groot, Saskia; Mailund, Thomas

    2007-01-01

    and pol are indeed annotated as such, we also discover several sites of less stringent negative selection within the env gene. The the best of our knowledge we are the first to subsequently provide a full selection annotation of the Hepatitis B genome by explicitly modelling the evolution within...... obtain an annotation of the coding regions, as well as a posterior probability for each site of the strength of selection acting on it. From this we may deduce the average posterior selection acting on the different genes. Whilst we are encouraged to see in HIV2, that the known to be conserved genes gag...

  17. Implementation of multistandard video signals integrator

    Science.gov (United States)

    Zabołotny, Wojciech M.; Pastuszak, Grzegorz; Sokół, Grzegorz; Borowik, Grzegorz; GÄ ska, Michał; Kasprowicz, Grzegorz H.; Poźniak, Krzysztof T.; Abramowski, Andrzej; Buchowicz, Andrzej; Trochimiuk, Maciej; Frasunek, Przemysław; Jurkiewicz, Rafał; Nalbach-Moszynska, Małgorzata; Wawrzusiak, Radosław; Bukowiecka, Danuta; Tyburska, Agata; Struniawski, Jarosław; Jastrzebski, Paweł; Jewartowski, BłaŻej; Brawata, Sebastian; Bubak, Iwona; Gloza, Małgorzata

    2017-08-01

    The paper describes the prototype implemetantion of the Video Signals Integrator (VSI). The function of the system is to integrate video signals from many sources. The VSI is a complex hybrid system consisting of hardware, firmware and software components. Its creation requires joint effort of experts from different areas. The VSI capture device is a portable hardware device responsible for capturing of video signals from different different sources and in various formats, and for transmitting them to the server. The NVR server aggregates video and control streams coming from different sources and multiplexes them into logical channels with each channel representing a single source. From there each channel can be distributed further to the end clients (consoles) for live display via a number of RTSP servers. The end client can, at the same time, inject control messages into a given channel to control movement of a CCTV camera.

  18. Video Production in the Classroom: Creating Success for Students and Schools.

    Science.gov (United States)

    Brown, Kenneth

    1993-01-01

    Describes benefits of integrating video production into high school curricula. Hardware requirements are suggested, including a camcorder, video cassette recorder, computer, software, converter, character generator, and editing machine; and typical video production projects are described, including a yearbook, documentaries, tutorials, music…

  19. From different angles : Exploring and applying the design potential of video

    NARCIS (Netherlands)

    Pasman, G.J.

    2012-01-01

    Recent developments in both hardware and software have brought video within the scope of design students as a new visual design tool. Being more and more equipped with cameras, for example in their smartphones, and video editing programs on their computers, they are increasing using video to record

  20. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  1. SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

    Science.gov (United States)

    Kolmogorov, Mikhail; Liu, Xiaowen; Pevzner, Pavel A

    2016-01-04

    In the past decade, proteogenomics has emerged as a valuable technique that contributes to the state-of-the-art in genome annotation; however, previous proteogenomic studies were limited to bottom-up mass spectrometry and did not take advantage of top-down approaches. We show that top-down proteogenomics allows one to address the problems that remained beyond the reach of traditional bottom-up proteogenomics. In particular, we show that top-down proteogenomics leads to the discovery of previously unannotated genes even in extensively studied bacterial genomes and present SpectroGene, a software tool for genome annotation using top-down tandem mass spectra. We further show that top-down proteogenomics searches (against the six-frame translation of a genome) identify nearly all proteoforms found in traditional top-down proteomics searches (against the annotated proteome). SpectroGene is freely available at http://github.com/fenderglass/SpectroGene .

  2. MIAWARE Software

    DEFF Research Database (Denmark)

    Wilkowski, Bartlomiej; Pereira, Oscar N. M.; Dias, Paulo

    2008-01-01

    This article presents MIAWARE, a software for Medical Image Analysis With Automated Reporting Engine, which was designed and developed for doctor/radiologist assistance. It allows to analyze an image stack from computed axial tomography scan of lungs (thorax) and, at the same time, to mark all...... pathologies on images and report their characteristics. The reporting process is normalized - radiologists cannot describe pathological changes with their own words, but can only use some terms from a specific vocabulary set provided by the software. Consequently, a normalized radiological report...... is automatically generated. Furthermore, MIAWARE software is accompanied with an intelligent search engine for medical reports, based on the relations between parts of the lungs. A logical structure of the lungs is introduced to the search algorithm through the specially developed ontology. As a result...

  3. Handling of Multimedia Files in the Invenio Software

    CERN Document Server

    Oltmanns, Björn; Schiefer, Bernhard

    ‘Handling of multimedia files in the Invenio Software’ is motivated by the need for integration of multimedia files in the open-source, large-scale digital library software Invenio, developed and used at CERN, the European Organisation for Nuclear Research. In the last years, digital assets like pictures, presentations podcasts and videos became abundant in these systems and digital libraries have grown out of their classic role of only storing bibliographical metadata. The thesis focuses on digital video as a type of multimedia and covers the complete workflow of handling video material in the Invenio software: from the ingestion of digital video material to its processing on to the storage and preservation and finally the streaming and presentation of videos to the user. The potential technologies to realise a video submission workflow are discussed in-depth and evaluated towards system integration with Invenio. The focus is set on open and free technologies, which can be redistributed with the Inve...

  4. Software survey

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2007-07-15

    This article presented a guide to new software applications designed to facilitate exploration, drilling and production activities. Oil and gas producers can use the proudcts for a range of functions, including reservoir characterization and accounting. In addition to a description of the software application, this article listed the name of software providers and the new features available in products. The featured software of Calgary-based providers included: PetroLOOK by Alcaro Softworks Inc.; ProphetFM and MasterDRIL by Advanced Measurements Inc.,; the EDGE screening tool by Canadian Discovery Ltd.; Emission Manager and Regulatory Document Manager by Envirosoft Corporation; ResSurveil, ResBalance and ResAssist by Epic Consulting Services Ltd; FAST WellTest and FAST RTA by Fekete Associates Inc.; OMNI 3D and VISTA 2D/3D by Gedco; VisualVoxAT, SBED and SBEDStudio by Geomodeling Technology Corporation; geoSCOUT, petroCUBE and gDC by GeoLOGIC Systems Ltd.; IHS Enerdeq Desktop and PETRA by IHS; DataVera by Intervera Data Solutions; FORGAS, PIPEFLO and WELLFLO by Neotechnology Consultants Ltd.; E and P Workflow Solutions by Neuralog Inc.; Oil and Gas Solutions by RiskAdvisory division of SAS; Petrel; GeoFrame, ECLIPSE, OFM, Osprey Risk and Avocet modeler, PIPESIM and Merak by Schlumberger Information Solutions; esi.manage and esi.executive by 3esi; and, dbAFE and PROSPECTOR by Winfund Corporation. Tower Management and Maintenance System, OverSite and Safety Orientation Management System software by Edmonton-based 3C Information Solutions Inc. were also highlighted along with PowerSHAPE, PowerMILL and FeatureCAM software by Windsor, Ontario-based Delcam. Software products by Texas-based companies featured in this article included the HTRI Xchanger Suite by Heat Transfer Research Inc.; Drillworks by Knowledge Systems; and GeoProbe, PowerView; GeoGraphix, AssetPlanner, Nexus software, Decision Management System, AssetSolver, and OpenWorks by Landmark; and, eVIN, Rig

  5. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries.

    Science.gov (United States)

    Smith, Robin P; Buchser, William J; Lemmon, Marcus B; Pardinas, Jose R; Bixby, John L; Lemmon, Vance P

    2008-04-10

    Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization. EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  6. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

    Directory of Open Access Journals (Sweden)

    Pardinas Jose R

    2008-04-01

    Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  7. Gait Analysis by Multi Video Sequence Analysis

    DEFF Research Database (Denmark)

    Jensen, Karsten; Juhl, Jens

    2009-01-01

    The project presented in this article aims to develop software so that close-range photogrammetry with sufficient accuracy can be used to point out the most frequent foot mal positions and monitor the effect of the traditional treatment. The project is carried out as a cooperation between...... the Orthopaedic Surgery in Northern Jutland and the Laboratory for Geoinformatics, Aalborg University. The superior requirements on the system are that it shall be without heavy expenses, be easy to install and easy to operate. A first version of the system is designed to measure the navicula height...... and the calcaneus angle during gait. In the introductory phase of the project the task has been to select, purchase and draw up hardware, select and purchase software concerning video streaming and to develop special software concerning automated registration of the position of the foot during gait by Multi Video...

  8. The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

    Science.gov (United States)

    Sayadi, Ahmed; Immonen, Elina; Bayram, Helen; Arnqvist, Göran

    2016-01-01

    Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.

  9. The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

    Directory of Open Access Journals (Sweden)

    Ahmed Sayadi

    Full Text Available Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant database and 13,382 were assigned to 34,100 Gene Ontology (GO terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.

  10. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...

  11. Temporal Annotation in the Clinical Domain

    Science.gov (United States)

    Styler, William F.; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet C; Erickson, Brad; Miller, Timothy; Lin, Chen; Savova, Guergana; Pustejovsky, James

    2014-01-01

    This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task. PMID:29082229

  12. Phage Genome Annotation Using the RAST Pipeline.

    Science.gov (United States)

    McNair, Katelyn; Aziz, Ramy Karam; Pusch, Gordon D; Overbeek, Ross; Dutilh, Bas E; Edwards, Robert

    2018-01-01

    Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.

  13. SASL: A Semantic Annotation System for Literature

    Science.gov (United States)

    Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai

    Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.

  14. GOTA: GO term annotation of biomedical literature

    National Research Council Canada - National Science Library

    Di Lena, Pietro; Domeniconi, Giacomo; Margara, Luciano; Moro, Gianluca

    2015-01-01

    .... Here we introduce GOTA, a GO term annotator for biomedical literature. The proposed approach makes use only of information that is readily available from public repositories and it is easily expandable to handle novel sources of information...

  15. Contributions to In Silico Genome Annotation

    KAUST Repository

    Kalkatawi, Manal M.

    2017-11-30

    Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation, while identifying functions of these regions is considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and timeconsuming. This study contributes to genome annotation by introducing several novel bioinformatics methods, some based on machine learning (ML) approaches. First, we present Dragon PolyA Spotter (DPS), a method for accurate identification of the polyadenylation signals (PAS) within human genomic DNA sequences. For this, we derived a novel feature-set able to characterize properties of the genomic region surrounding the PAS, enabling development of high accuracy optimized ML predictive models. DPS considerably outperformed the state-of-the-art results. The second contribution concerns developing generic models for structural annotation, i.e., the recognition of different genomic signals and regions (GSR) within eukaryotic DNA. We developed DeepGSR, a systematic framework that facilitates generating ML models to predict GSR with high accuracy. To the best of our knowledge, no available generic and automated method exists for such task that could facilitate the studies of newly sequenced organisms. The prediction module of DeepGSR uses deep learning algorithms to derive highly abstract features that depend mainly on proper data representation and hyperparameters calibration. DeepGSR, which was evaluated on recognition of PAS and translation initiation sites (TIS) in different organisms, yields a simpler and more precise representation of the problem under study, compared to some other hand-tailored models, while producing high accuracy prediction results. Finally

  16. [Software version and medical device software supervision].

    Science.gov (United States)

    Peng, Liang; Liu, Xiaoyan

    2015-01-01

    The importance of software version in the medical device software supervision does not cause enough attention at present. First of all, the effect of software version in the medical device software supervision is discussed, and then the necessity of software version in the medical device software supervision is analyzed based on the discussion of the misunderstanding of software version. Finally the concrete suggestions on software version naming rules, software version supervision for the software in medical devices, and software version supervision scheme are proposed.

  17. Designing and Using Videos in Undergraduate Geoscience Education - a workshop and resource website review

    Science.gov (United States)

    Wiese, K.; Mcconnell, D. A.

    2014-12-01

    Do you use video in your teaching? Do you make your own video? Interested in joining our growing community of geoscience educators designing and using video inside and outside the classroom? Over four months in Spring 2014, 22 educators of varying video design and development expertise participated in an NSF-funded On the Cutting Edge virtual workshop to review the best educational research on video design and use; to share video-development/use strategies and experiences; and to develop a website of resources for a growing community of geoscience educators who use video: http://serc.carleton.edu/NAGTWorkshops/video/workshop2014/index.html. The site includes links to workshop presentations, teaching activity collections, and a growing collection of online video resources, including "How-To" videos for various video editing or video-making software and hardware options. Additional web resources support several topical themes including: using videos to flip classes, handling ADA access and copyright issues, assessing the effectiveness of videos inside and outside the classroom, best design principles for video learning, and lists and links of the best videos publicly available for use. The workshop represents an initial step in the creation of an informal team of collaborators devoted to the development and support of an ongoing network of geoscience educators designing and using video. Instructors who are interested in joining this effort are encouraged to contact the lead author.

  18. Genepi: a blackboard framework for genome annotation

    Science.gov (United States)

    Descorps-Declère, Stéphane; Ziébelin, Danielle; Rechenmann, François; Viari, Alain

    2006-01-01

    Background Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures. Conclusion In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process. PMID:17038181

  19. Genepi: a blackboard framework for genome annotation

    Directory of Open Access Journals (Sweden)

    Ziébelin Danielle

    2006-10-01

    Full Text Available Abstract Background Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data or methodological (new methods knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results We have implemented a blackboard framework (called Genepi for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures. Conclusion In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied and opportunistic (the flow of execution depends on the state of our knowledge aspects of the annotation process.

  20. Gene Ontology (GO) Annotation in Biomedical Literature

    OpenAIRE

    Gálvez, Carmen

    2008-01-01

    In this paper, we propose an approach for doing Gene Ontology (GO) annotation on biomedical texts. The GO is an effort to create a controlled terminology for labelling gene functions in a more precise. Our system is based on the application of Parametrized Finite-State Graphs (P-FSG) for GO tagging. This process was implemented to the annotation of genes related with Alzehimer disease. This prototype is an undergoing work, in the future should be evaluated to verify its value

  1. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... to layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  2. Software Reviews.

    Science.gov (United States)

    Science Software Quarterly, 1984

    1984-01-01

    Provides extensive reviews of computer software, examining documentation, ease of use, performance, error handling, special features, and system requirements. Includes statistics, problem-solving (TK Solver), label printing, database management, experimental psychology, Encyclopedia Britannica biology, and DNA-sequencing programs. A program for…

  3. Software Reviews.

    Science.gov (United States)

    Mathematics and Computer Education, 1987

    1987-01-01

    Presented are reviews of several microcomputer software programs. Included are reviews of: (1) Microstat (Zenith); (2) MathCAD (MathSoft); (3) Discrete Mathematics (True Basic); (4) CALCULUS (True Basic); (5) Linear-Kit (John Wiley); and (6) Geometry Sensei (Broderbund). (RH)

  4. Software Modernization.

    Science.gov (United States)

    1986-05-01

    is desirable to automate these error-prone tasks to the maximum extent practica ble. For even modestly-sized software activities, the costs of auto...22161. (703) 487 4848. FY Fiscal Year (I October - 30 September) IIQ Headquarters IEEE Institute or Electrical and Electronics Engineers %ON, JOVIAL A

  5. Software Architecture

    NARCIS (Netherlands)

    Tekinerdogan, B.; Zdun, Uwe; Babar, Ali

    2016-01-01

    This book constitutes the proceedings of the 10th European Conference on Software Architecture, ECSA 2016, held in Copenhagen, Denmark, in November/December 2016.

    The 13 full papers presented together with 12 short papers were carefully reviewed and selected from 84 submissions. They are

  6. nGASP - the nematode genome annotation assessment project

    Energy Technology Data Exchange (ETDEWEB)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

  7. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

    Science.gov (United States)

    Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

  8. Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

    Science.gov (United States)

    Wang, Qinghua; Arighi, Cecilia N.; King, Benjamin L.; Polson, Shawn W.; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F.; Page, Shallee T.; Farnum Rendino, Marc; Thomas, William Kelley; Udwary, Daniel W.; Wu, Cathy H.

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome. PMID:22434832

  9. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  10. DAS Writeback: A Collaborative Annotation System

    Directory of Open Access Journals (Sweden)

    Garcia Alexander

    2011-05-01

    Full Text Available Abstract Background Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations. Results We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task. Conclusions We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.

  11. Automated clinical annotation of tissue bank specimens.

    Science.gov (United States)

    Gilbertson, John R; Gupta, Rajnish; Nie, Yimin; Patel, Ashokkumar A; Becich, Michael J

    2004-01-01

    Modern, molecular bio-medicine is driving a growing demand for extensively annotated tissue bank specimens. With careful clinical, pathologic and outcomes annotation, samples can be better matched to the research question at hand and experimental results better understood and verified. However, the difficulty and expense of detailed specimen annotation is well beyond the capability of most banks and has made access to well documented tissue a major limitation in medical re-search. In this context, we have implemented automated annotation of banked tissue by integrating data from three clinical systems--the cancer registry, the pathology LIS and the tissue bank inventory system--through a classical data warehouse environment. The project required modification of clinical systems, development of methods to identify patients between and map data elements across systems and the creation of de-identified data in data marts for use by researchers. The result has been much more extensive and accurate initial tissue annotation with less effort in the tissue bank, as well as dynamic ongoing annotation as the cancer registry follows patients over time.

  12. GOTA: GO term annotation of biomedical literature.

    Science.gov (United States)

    Di Lena, Pietro; Domeniconi, Giacomo; Margara, Luciano; Moro, Gianluca

    2015-10-28

    Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes by using published literature. The annotation task is extremely time-consuming, therefore there is an increasing interest in automated tools that can assist human experts. Here we introduce GOTA, a GO term annotator for biomedical literature. The proposed approach makes use only of information that is readily available from public repositories and it is easily expandable to handle novel sources of information. We assess the classification capabilities of GOTA on a large benchmark set of publications. The overall performances are encouraging in comparison to the state of the art in multi-label classification over large taxonomies. Furthermore, the experimental tests provide some interesting insights into the potential improvement of automated annotation tools. GOTA implements a flexible and expandable model for GO annotation of biomedical literature. The current version of the GOTA tool is freely available at http://gota.apice.unibo.it.

  13. Enhancing student interactions with the instructor and content using pen-based technology, YouTube videos, and virtual conferencing.

    Science.gov (United States)

    Cox, James R

    2011-01-01

    This report describes the incorporation of digital learning elements in organic chemistry and biochemistry courses. The first example is the use of pen-based technology and a large-format PowerPoint slide to construct a map that integrates various metabolic pathways and control points. Students can use this map to visualize the integrated nature of metabolism and how various hormones impact metabolic regulation. The second example is the embedding of health-related YouTube videos directly into PowerPoint presentations. These videos become a part of the course notes and can be viewed within PowerPoint as long as students are online. The third example is the use of a webcam to show physical models during online sessions using web-conferencing software. Various molecular conformations can be shown through the webcam, and snapshots of important conformations can be incorporated into the notes for further discussion and annotation. Each of the digital learning elements discussed in this report is an attempt to use technology to improve the quality of educational resources available outside of the classroom to foster student engagement with ideas and concepts. Biochemistry and Molecular Biology Education Vol. 39, No. 1, pp. 4-9, 2011. Copyright © 2011 Wiley Periodicals, Inc.

  14. Software Accelerates Computing Time for Complex Math

    Science.gov (United States)

    2014-01-01

    Ames Research Center awarded Newark, Delaware-based EM Photonics Inc. SBIR funding to utilize graphic processing unit (GPU) technology- traditionally used for computer video games-to develop high-computing software called CULA. The software gives users the ability to run complex algorithms on personal computers with greater speed. As a result of the NASA collaboration, the number of employees at the company has increased 10 percent.

  15. Innovations in Computing Sciences and Software Engineering

    CERN Document Server

    Sobh, Tarek

    2010-01-01

    "Innovations in Computing Sciences and Software Engineering" includes a set of rigorously reviewed world-class manuscripts addressing and detailing state-of-the-art research projects in the areas of Computer Science, Software Engineering, Computer Engineering, and Systems Engineering and Sciences. The topics covered include: Image and Pattern Recognition: Compression, Image processing, Signal Processing Architectures, Signal Processing for Communication, Signal Processing Implementation, Speech Compression, and Video Coding Architectures; Languages and Systems: Algorithms, Databases,

  16. A simplified 2D to 3D video conversion technology——taking virtual campus video production as an example

    Directory of Open Access Journals (Sweden)

    ZHUANG Huiyang

    2012-10-01

    Full Text Available This paper describes a simplified 2D to 3D Video Conversion Technology, taking virtual campus 3D video production as an example. First, it clarifies the meaning of the 2D to 3D Video Conversion Technology, and points out the disadvantages of traditional methods. Second, it forms an innovative and convenient method. A flow diagram, software and hardware configurations are presented. Finally, detailed description of the conversion steps and precautions are given in turn to the three processes, namely, preparing materials, modeling objects and baking landscapes, recording screen and converting videos .

  17. GeneTools – application for functional annotation and statistical hypothesis testing

    Directory of Open Access Journals (Sweden)

    Langaas Mette

    2006-10-01

    Full Text Available Abstract Background Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions. Results GeneTools is a web-service providing access to a database that brings together information from a broad range of resources. The annotation data are updated weekly, guaranteeing that users get data most recently available. Data submitted by the user are stored in the database, where it can easily be updated, shared between users and exported in various formats. GeneTools provides three different tools: i NMC Annotation Tool, which offers annotations from several databases like UniGene, Entrez Gene, SwissProt and GeneOntology, in both single- and batch search mode. ii GO Annotator Tool, where users can add new gene ontology (GO annotations to genes of interest. These user defined GO annotations can be used in further analysis or exported for public distribution. iii eGOn, a tool for visualization and statistical hypothesis testing of GO category representation. As the first GO tool, eGOn supports hypothesis testing for three different situations (master-target situation, mutually exclusive target-target situation and intersecting target-target situation. An important additional function is an evidence-code filter that allows users, to select the GO annotations for the

  18. Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.

    Science.gov (United States)

    McKain, Michael R; Hartsock, Ryan H; Wohl, Molly M; Kellogg, Elizabeth A

    2017-01-01

    Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/ It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  19. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... support group for me? Find a Group Upcoming Events Video Library Photo Gallery One-on-One Support ... group for me? Find a group Back Upcoming events Video Library Photo Gallery One-on-One Support ...

  20. Video Games and Citizenship

    National Research Council Canada - National Science Library

    Bourgonjon, Jeroen; Soetaert, Ronald

    2013-01-01

    ... by exploring a particular aspect of digitization that affects young people, namely video games. They explore the new social spaces which emerge in video game culture and how these spaces relate to community building and citizenship...

  1. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... Doctor Find a Provider Meet the Team Blog Articles News Resources Links Videos Podcasts Webinars For the ... Doctor Find a Provider Meet the Team Blog Articles News Provider Directory Donate Resources Links Videos Podcasts ...

  2. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... Doctor Find a Provider Meet the Team Blog Articles & Stories News Resources Links Videos Podcasts Webinars For ... Doctor Find a Provider Meet the Team Blog Articles & Stories News Provider Directory Donate Resources Links Videos ...

  3. Digital Video in Research

    DEFF Research Database (Denmark)

    Frølunde, Lisbeth

    2012-01-01

    questions of our media literacy pertaining to authoring multimodal texts (visual, verbal, audial, etc.) in research practice and the status of multimodal texts in academia. The implications of academic video extend to wider issues of how researchers harness opportunities to author different types of texts......Is video becoming “the new black” in academia, if so, what are the challenges? The integration of video in research methodology (for collection, analysis) is well-known, but the use of “academic video” for dissemination is relatively new (Eriksson and Sørensen). The focus of this paper is academic...... video, or short video essays produced for the explicit purpose of communicating research processes, topics, and research-based knowledge (see the journal of academic videos: www.audiovisualthinking.org). Video is increasingly used in popular showcases for video online, such as YouTube and Vimeo, as well...

  4. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... Back Support Groups Is a support group for me? Find a Group Upcoming Events Video Library Photo ... Support Groups Back Is a support group for me? Find a group Back Upcoming events Video Library ...

  5. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... group for me? Find a Group Upcoming Events Video Library Photo Gallery One-on-One Support ANetwork ... for me? Find a group Back Upcoming events Video Library Photo Gallery One-on-One Support Back ...

  6. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... the Team Blog Articles & Stories News Resources Links Videos Podcasts Webinars For the Media For Clinicians For ... Family Caregivers Glossary Menu In this section Links Videos Podcasts Webinars For the Media For Clinicians For ...

  7. Videos, Podcasts and Livechats

    Science.gov (United States)

    ... the Team Blog Articles & Stories News Resources Links Videos Podcasts Webinars For the Media For Clinicians For ... Family Caregivers Glossary Menu In this section Links Videos Podcasts Webinars For the Media For Clinicians For ...

  8. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... a Provider Meet the Team Blog Articles & Stories News Resources Links Videos Podcasts Webinars For the Media ... a Provider Meet the Team Blog Articles & Stories News Provider Directory Donate Resources Links Videos Podcasts Webinars ...

  9. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... for me? Find a Group Upcoming Events Video Library Photo Gallery One-on-One Support ANetwork Peer ... me? Find a group Back Upcoming events Video Library Photo Gallery One-on-One Support Back ANetwork ...

  10. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... News Resources Links Videos Podcasts Webinars For the Media For Clinicians For Policymakers For Family Caregivers Glossary ... this section Links Videos Podcasts Webinars For the Media For Clinicians For Policymakers For Family Caregivers Glossary ...

  11. Reviews Book: Extended Project Student Guide Book: My Inventions Book: ASE Guide to Research in Science Education Classroom Video: The Science of Starlight Software: SPARKvue Book: The Geek Manifesto Ebook: A Big Ball of Fire Apps

    Science.gov (United States)

    2014-05-01

    WE RECOMMEND Level 3 Extended Project Student Guide A non-specialist, generally useful and nicely put together guide to project work ASE Guide to Research in Science Education Few words wasted in this handy introduction and reference The Science of Starlight Slow but steady DVD covers useful ground SPARKvue Impressive software now available as an app WORTH A LOOK My Inventions and Other Writings Science, engineering, autobiography, visions and psychic phenomena mixed in a strange but revealing concoction The Geek Manifesto: Why Science Matters More enthusiasm than science, but a good motivator and interesting A Big Ball of Fire: Your questions about the Sun answered Free iTunes download made by and for students goes down well APPS Collider visualises LHC experiments ... Science Museum app enhances school trips ... useful information for the Cambridge Science Festival

  12. Climate Science Communications - Video Visualization Techniques

    Science.gov (United States)

    Reisman, J. P.; Mann, M. E.

    2010-12-01

    Communicating Climate science is challenging due to it's complexity. But as they say, a picture is worth a thousand words. Visualization techniques can be merely graphical or combine multimedia so as to make graphs come alive in context with other visual and auditory cues. This can also make the information come alive in a way that better communicates what the science is all about. What types of graphics to use depends on your audience, some graphs are great for scientists but if you are trying to communicate to a less sophisticated audience, certain visuals translate information in a more easily perceptible manner. Hollywood techniques and style can be applied to these graphs to give them even more impact. Video is one of the most powerful communication tools in its ability to combine visual and audio through time. Adding music and visual cues such as pans and zooms can greatly enhance the ability to communicate your concepts. Video software ranges from relatively simple to very sophisticated. In reality, you don't need the best tools to get your point across. In fact, with relatively inexpensive software, you can put together powerful videos that more effectively convey the science you are working on with greater sophistication, and in an entertaining way. We will examine some basic techniques to increase the quality of video visualization to make it more effective in communicating complexity. If a picture is worth a thousand words, a decent video with music, and a bit of narration is priceless.

  13. How Online Access Changed Amateur Video Editing

    Directory of Open Access Journals (Sweden)

    Eugster Benjamin

    2014-12-01

    Full Text Available Digital technology has often been discussed in relation to how it changed either the production or the reception of audiovisual cultures. This paper will consider a combination of both as a crucial part in understanding strategies of inter- and transmedial amateur creativity. Based on an experimental ethnography of the online video subgenre/subculture “YouTubePoop,” the paper will elaborate on the connection between the individual experience and the creation of digital media. The loose collective of independent amateurs behind the YouTubePoop videos makes use of already existing audiovisual material ranging from television shows to videos of other YouTube users. The re-created remixes and mash-ups are characterized by their random selection of original material and their nonsensical humour. Hence, the rapid montage of this heterogeneous content is just as much part of the intensified aesthetic expressiveness as are the applied special effects available in the digital video editing software. Both aspects highlight the strong interdependence of the rapid accessibility of online content and digital technology and the new aesthetic expressions they are fostering. The paper will show how the experience and navigation of digital interfaces (editing software, media players, or homepages affect the design and practice of these video-remixes. This will open the discussion about intertextual strategies of media appropriation to an aesthetic and praxeological analysis of media interaction.

  14. Discovering gene annotations in biomedical text databases

    Directory of Open Access Journals (Sweden)

    Ozsoyoglu Gultekin

    2008-03-01

    Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

  15. Transmission of compressed video

    Science.gov (United States)

    Pasch, H. L.

    1990-09-01

    An overview of video coding is presented. The aim is not to give a technical summary of possible coding techniques, but to address subjects related to video compression in general and to the transmission of compressed video in more detail. Bit rate reduction is in general possible by removing redundant information; removing information the eye does not use anyway; and reducing the quality of the video. The codecs which are used for reducing the bit rate, can be divided into two groups: Constant Bit rate Codecs (CBC's), which keep the bit rate constant, but vary the video quality; and Variable Bit rate Codecs (VBC's), which keep the video quality constant by varying the bit rate. VBC's can be in general reach a higher video quality than CBC's using less bandwidth, but need a transmission system that allows the bandwidth of a connection to fluctuate in time. The current and the next generation of the PSTN does not allow this; ATM might. There are several factors which influence the quality of video: the bit error rate of the transmission channel, slip rate, packet loss rate/packet insertion rate, end-to-end delay, phase shift between voice and video, and bit rate. Based on the bit rate of the coded video, the following classification of coded video can be made: High Definition Television (HDTV); Broadcast Quality Television (BQTV); video conferencing; and video telephony. The properties of these classes are given. The video conferencing and video telephony equipment available now and in the next few years can be divided into three categories: conforming to 1984 CCITT standard for video conferencing; conforming to 1988 CCITT standard; and conforming to no standard.

  16. Making good physics videos

    Science.gov (United States)

    Lincoln, James

    2017-05-01

    Online videos are an increasingly important way technology is contributing to the improvement of physics teaching. Students and teachers have begun to rely on online videos to provide them with content knowledge and instructional strategies. Online audiences are expecting greater production value, and departments are sometimes requesting educators to post video pre-labs or to flip our classrooms. In this article, I share my advice on creating engaging physics videos.

  17. Desktop video conferencing

    OpenAIRE

    Potter, Ray; Roberts, Deborah

    2007-01-01

    This guide aims to provide an introduction to Desktop Video Conferencing. You may be familiar with video conferencing, where participants typically book a designated conference room and communicate with another group in a similar room on another site via a large screen display. Desktop video conferencing (DVC), as the name suggests, allows users to video conference from the comfort of their own office, workplace or home via a desktop/laptop Personal Computer. DVC provides live audio and visua...

  18. From different angles: Exploring and applying the design potential of video

    OpenAIRE

    Pasman, G.J.

    2012-01-01

    Recent developments in both hardware and software have brought video within the scope of design students as a new visual design tool. Being more and more equipped with cameras, for example in their smartphones, and video editing programs on their computers, they are increasing using video to record their research activities or present their design ideas. In design education, however, the full potential of video as a rich and contextual design medium is yet to be explored and developed. This p...

  19. annot8r: GO, EC and KEGG annotation of EST datasets

    Directory of Open Access Journals (Sweden)

    Schmid Ralf

    2008-04-01

    Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non

  20. 47 CFR 79.3 - Video description of video programming.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Video description of video programming. 79.3... CLOSED CAPTIONING AND VIDEO DESCRIPTION OF VIDEO PROGRAMMING § 79.3 Video description of video programming. (a) Definitions. For purposes of this section the following definitions shall apply: (1...

  1. Video Self-Modeling

    Science.gov (United States)

    Buggey, Tom; Ogle, Lindsey

    2012-01-01

    Video self-modeling (VSM) first appeared on the psychology and education stage in the early 1970s. The practical applications of VSM were limited by lack of access to tools for editing video, which is necessary for almost all self-modeling videos. Thus, VSM remained in the research domain until the advent of camcorders and VCR/DVD players and,…

  2. Tracing Sequential Video Production

    DEFF Research Database (Denmark)

    Otrel-Cass, Kathrin; Khalid, Md. Saifuddin

    2015-01-01

    With an interest in learning that is set in collaborative situations, the data session presents excerpts from video data produced by two of fifteen students from a class of 5th semester techno-anthropology course. Students used video cameras to capture the time they spent working with a scientist...... video, nature of the interactional space, and material and spatial semiotics....

  3. Calculation Software

    Science.gov (United States)

    1994-01-01

    MathSoft Plus 5.0 is a calculation software package for electrical engineers and computer scientists who need advanced math functionality. It incorporates SmartMath, an expert system that determines a strategy for solving difficult mathematical problems. SmartMath was the result of the integration into Mathcad of CLIPS, a NASA-developed shell for creating expert systems. By using CLIPS, MathSoft, Inc. was able to save the time and money involved in writing the original program.

  4. Software preservation

    Directory of Open Access Journals (Sweden)

    Tadej Vodopivec

    2011-01-01

    Full Text Available Comtrade Ltd. covers a wide range of activities related to information and communication technologies; its deliverables include web applications, locally installed programs,system software, drivers, embedded software (used e.g. in medical devices, auto parts,communication switchboards. Also the extensive knowledge and practical experience about digital long-term preservation technologies have been acquired. This wide spectrum of activities puts us in the position to discuss the often overlooked aspect of the digital preservation - preservation of software programs. There are many resources dedicated to digital preservation of digital data, documents and multimedia records,but not so many about how to preserve the functionalities and features of computer programs. Exactly these functionalities - dynamic response to inputs - render the computer programs rich compared to documents or linear multimedia. The article opens the questions on the beginning of the way to the permanent digital preservation. The purpose is to find a way in the right direction, where all relevant aspects will be covered in proper balance. The following questions are asked: why at all to preserve computer programs permanently, who should do this and for whom, when we should think about permanent program preservation, what should be persevered (such as source code, screenshots, documentation, and social context of the program - e.g. media response to it ..., where and how? To illustrate the theoretic concepts given the idea of virtual national museum of electronic banking is also presented.

  5. Video signals integrator (VSI) system architecture

    Science.gov (United States)

    Kasprowicz, Grzegorz; Pastuszak, Grzegorz; Poźniak, Krzysztof; Trochimiuk, Maciej; Abramowski, Andrzej; Gaska, Michal; Bukowiecka, Danuta; Tyburska, Agata; Struniawski, Jarosław; Jastrzebski, Pawel; Jewartowski, Blazej; Frasunek, Przemysław; Nalbach-Moszynska, Małgorzata; Brawata, Sebastian; Bubak, Iwona; Gloza, Małgorzata

    2016-09-01

    The purpose of the project is development of a platform which integrates video signals from many sources. The signals can be sourced by existing analogue CCTV surveillance installations, recent internet-protocol (IP) cameras or single cameras of any type. The system will consist of portable devices that provide conversion, encoding, transmission and archiving. The sharing subsystem will use distributed file system and also user console which provides simultaneous access to any of video streams in real time. The system is fully modular so its extension is possible, both from hardware and software side. Due to standard modular technology used, partial technology modernization is also possible during a long exploitation period.

  6. A video rate laser scanning confocal microscope

    Science.gov (United States)

    Ma, Hongzhou; Jiang, James; Ren, Hongwu; Cable, Alex E.

    2008-02-01

    A video-rate laser scanning microscope was developed as an imaging engine to integrate with other photonic building blocks to fulfill various microscopic imaging applications. The system is quipped with diode laser source, resonant scanner, galvo scanner, control electronic and computer loaded with data acquisition boards and imaging software. Based on an open frame design, the system can be combined with varies optics to perform the functions of fluorescence confocal microscopy, multi-photon microscopy and backscattering confocal microscopy. Mounted to the camera port, it allows a traditional microscope to obtain confocal images at video rate. In this paper, we will describe the design principle and demonstrate examples of applications.

  7. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  8. Semi-Semantic Annotation: A guideline for the URDU.KON-TB treebank POS annotation

    Directory of Open Access Journals (Sweden)

    Qaiser ABBAS

    2016-12-01

    Full Text Available This work elaborates the semi-semantic part of speech annotation guidelines for the URDU.KON-TB treebank: an annotated corpus. A hierarchical annotation scheme was designed to label the part of speech and then applied on the corpus. This raw corpus was collected from the Urdu Wikipedia and the Jang newspaper and then annotated with the proposed semi-semantic part of speech labels. The corpus contains text of local & international news, social stories, sports, culture, finance, religion, traveling, etc. This exercise finally contributed a part of speech annotation to the URDU.KON-TB treebank. Twenty-two main part of speech categories are divided into subcategories, which conclude the morphological, and semantical information encoded in it. This article reports the annotation guidelines in major; however, it also briefs the development of the URDU.KON-TB treebank, which includes the raw corpus collection, designing & employment of annotation scheme and finally, its statistical evaluation and results. The guidelines presented as follows, will be useful for linguistic community to annotate the sentences not only for the national language Urdu but for the other indigenous languages like Punjab, Sindhi, Pashto, etc., as well.

  9. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

    Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  10. A Web-based High-Throughput Tool for Next-Generation Sequence Annotation

    Science.gov (United States)

    2011-06-01

    developed for high-quality, automated annotation of bacterial genomes. These include BASys[8], RAST [9], and Microbial Genomes Database Web resources[10] as...present the results of the parallel processing performance testing of AGeS as well as of the software validation experiments. 3.1 Parallel Performance To...parallelized and is currently operational at the Mana Linux cluster at the MHPCC, where we performed scalability tests and found that a 2.2-Mbp bacterial

  11. Training value of laparoscopic colorectal videos on the World Wide Web: a pilot study on the educational quality of laparoscopic right hemicolectomy videos.

    Science.gov (United States)

    Celentano, V; Browning, M; Hitchins, C; Giglio, M C; Coleman, M G

    2017-11-01

    Instructive laparoscopy videos with appropriate exposition could be ideal for initial training in laparoscopic surgery, but unfortunately there are no guidelines for annotating these videos or agreed methods to measure the educational content and the safety of the procedure presented. Aim of this study is to systematically search the World Wide Web to determine the availability of laparoscopic colorectal surgery videos and to objectively establish their potential training value. A search for laparoscopic right hemicolectomy videos was performed on the three most used English language web search engines Google.com, Bing.com, and Yahoo.com; moreover, a survey among 25 local trainees was performed to identify additional websites for inclusion. All laparoscopic right hemicolectomy videos with an English language title were included. Videos of open surgery, single incision laparoscopic surgery, robotic, and hand-assisted surgery were excluded. The safety of the demonstrated procedure was assessed with a validated competency assessment tool specifically designed for laparoscopic colorectal surgery and data on the educational content of the video were extracted. Thirty-one websites were identified and 182 surgical videos were included. One hundred and seventy-three videos (95%) detailed the year of publication; this demonstrated a significant increase in the number of videos published per year from 2009. Characteristics of the patient were rarely presented, only 10 videos (5.4%) reported operating time and only 6 videos (3.2%) reported 30-day morbidity; 34 videos (18.6%) underwent a peer-review process prior to publication. Formal case presentation, the presence of audio narration, the use of diagrams, and snapshots and a step-by-step approach are all characteristics of peer-reviewed videos but no significant difference was found in the safety of the procedure. Laparoscopic videos can be a useful adjunct to operative training. There is a large and increasing amount of

  12. Advanced video coding systems

    CERN Document Server

    Gao, Wen

    2015-01-01

    This comprehensive and accessible text/reference presents an overview of the state of the art in video coding technology. Specifically, the book introduces the tools of the AVS2 standard, describing how AVS2 can help to achieve a significant improvement in coding efficiency for future video networks and applications by incorporating smarter coding tools such as scene video coding. Topics and features: introduces the basic concepts in video coding, and presents a short history of video coding technology and standards; reviews the coding framework, main coding tools, and syntax structure of AV

  13. Intelligent video surveillance systems

    CERN Document Server

    Dufour, Jean-Yves

    2012-01-01

    Belonging to the wider academic field of computer vision, video analytics has aroused a phenomenal surge of interest since the current millennium. Video analytics is intended to solve the problem of the incapability of exploiting video streams in real time for the purpose of detection or anticipation. It involves analyzing the videos using algorithms that detect and track objects of interest over time and that indicate the presence of events or suspect behavior involving these objects.The aims of this book are to highlight the operational attempts of video analytics, to identify possi

  14. VBR video traffic models

    CERN Document Server

    Tanwir, Savera

    2014-01-01

    There has been a phenomenal growth in video applications over the past few years. An accurate traffic model of Variable Bit Rate (VBR) video is necessary for performance evaluation of a network design and for generating synthetic traffic that can be used for benchmarking a network. A large number of models for VBR video traffic have been proposed in the literature for different types of video in the past 20 years. Here, the authors have classified and surveyed these models and have also evaluated the models for H.264 AVC and MVC encoded video and discussed their findings.

  15. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

    Science.gov (United States)

    Arnaiz, Olivier; Van Dijk, Erwin; Bétermier, Mireille; Lhuillier-Akakpo, Maoussi; de Vanssay, Augustin; Duharcourt, Sandra; Sallet, Erika; Gouzy, Jérôme; Sperling, Linda

    2017-06-26

    The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3' and 5' UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis

  16. Machine learning annotation of human branchpoints.

    Science.gov (United States)

    Signal, Bethany; Gloss, Brian S; Dinger, Marcel E; Mercer, Tim R

    2017-10-28

    The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to the difficulty in experimentally identifying these splicing elements. To address this limitation, we have developed a machine-learning algorithm - branchpointer - to identify branchpoint elements solely from gene annotations and genomic sequence. Using branchpointer, we annotate branchpoint elements in 85% of human gene introns with sensitivity (61.8%) and specificity (97.8%). In addition to annotation, branchpointer can evaluate the impact of SNPs on branchpoint architecture to inform functional interpretation of genetic variants. Branchpointer identifies all published deleterious branchpoint mutations annotated in clinical variant databases, and finds thousands of additional clinical and common genetic variants with similar predicted effects. This genome-wide annotation of branchpoints provides a reference for the genetic analysis of splicing, and the interpretation of noncoding variation. Branchpointer is written and implemented in the statistical programming language R and is freely available under a BSD license as a package through Bioconductor. b.signal@garvan.org.au. Supplementary data are available at Bioinformatics online.

  17. Active learning reduces annotation time for clinical concept extraction.

    Science.gov (United States)

    Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

    2017-10-01

    To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. orchid: a novel management, annotation, and machine learning framework for analyzing cancer mutations.

    Science.gov (United States)

    Cario, Clinton L; Witte, John S

    2017-11-02

    As whole-genome tumor sequence and biological annotation datasets grow in size, number, and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments, and machine learning algorithms, there is also a need for the integration of functionality across frameworks. We present orchid, a python based software package for the management, annotation, and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage, and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier. Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid. Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution. clint.cario@ucsf.edu or john.witte@ucsf.edu. Supplementary data are available at Bioinformatics online.

  19. Flip Video for Dummies

    CERN Document Server

    Hutsko, Joe

    2010-01-01

    The full-color guide to shooting great video with the Flip Video camera. The inexpensive Flip Video camera is currently one of the hottest must-have gadgets. It's portable and connects easily to any computer to transfer video you shoot onto your PC or Mac. Although the Flip Video camera comes with a quick-start guide, it lacks a how-to manual, and this full-color book fills that void! Packed with full-color screen shots throughout, Flip Video For Dummies shows you how to shoot the best possible footage in a variety of situations. You'll learn how to transfer video to your computer and then edi

  20. Video Altimeter and Obstruction Detector for an Aircraft

    Science.gov (United States)

    Delgado, Frank J.; Abernathy, Michael F.; White, Janis; Dolson, William R.

    2013-01-01

    Video-based altimetric and obstruction detection systems for aircraft have been partially developed. The hardware of a system of this type includes a downward-looking video camera, a video digitizer, a Global Positioning System receiver or other means of measuring the aircraft velocity relative to the ground, a gyroscope based or other attitude-determination subsystem, and a computer running altimetric and/or obstruction-detection software. From the digitized video data, the altimetric software computes the pixel velocity in an appropriate part of the video image and the corresponding angular relative motion of the ground within the field of view of the camera. Then by use of trigonometric relationships among the aircraft velocity, the attitude of the camera, the angular relative motion, and the altitude, the software computes the altitude. The obstruction-detection software performs somewhat similar calculations as part of a larger task in which it uses the pixel velocity data from the entire video image to compute a depth map, which can be correlated with a terrain map, showing locations of potential obstructions. The depth map can be used as real-time hazard display and/or to update an obstruction database.

  1. MannDB: A microbial annotation database for protein characterization

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C; Lam, M; Smith, J; Zemla, A; Dyer, M; Kuczmarski, T; Vitalis, E; Slezak, T

    2006-05-19

    MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high

  2. Software Epistemology

    Science.gov (United States)

    2016-03-01

    in-vitro decision to incubate a startup, Lexumo [7], which is developing a commercial Software as a Service (SaaS) vulnerability assessment...reduction and technology exploration as well as incubated a commercial offering with Draper white-label support to DoD and IC customers—dramatically...Figure 9. OpHash Map 1.3.7 Opcode Hash (OpHash) A custom hashing scheme was developed in our SWE research to enable fast, but fuzzy , matching of basic

  3. Annotating images by mining image search results.

    Science.gov (United States)

    Wang, Xin-Jing; Zhang, Lei; Li, Xirong; Ma, Wei-Ying

    2008-11-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results. Some 2.4 million images with their surrounding text are collected from a few photo forums to support this approach. The entire process is formulated in a divide-and-conquer framework where a query keyword is provided along with the uncaptioned image to improve both the effectiveness and efficiency. This is helpful when the collected data set is not dense everywhere. In this sense, our approach contains three steps: 1) the search process to discover visually and semantically similar search results, 2) the mining process to identify salient terms from textual descriptions of the search results, and 3) the annotation rejection process to filter out noisy terms yielded by Step 2. To ensure real-time annotation, two key techniques are leveraged-one is to map the high-dimensional image visual features into hash codes, the other is to implement it as a distributed system, of which the search and mining processes are provided as Web services. As a typical result, the entire process finishes in less than 1 second. Since no training data set is required, our approach enables annotating with unlimited vocabulary and is highly scalable and robust to outliers. Experimental results on both real Web images and a benchmark image data set show the effectiveness and efficiency of the proposed algorithm. It is also worth noting that, although the entire approach is illustrated within the divide-and conquer framework, a query keyword is not crucial to our current implementation. We provide experimental results to prove this.

  4. Corpus annotation for mining biomedical events from literature

    Directory of Open Access Journals (Sweden)

    Tsujii Jun'ichi

    2008-01-01

    Full Text Available Abstract Background Advanced Text Mining (TM such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech, syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1 to design a scheme of annotation which meets specific requirements of text annotation, (2 to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3 to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing-based TM in the bio-medical domain.

  5. GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.

    Science.gov (United States)

    Young, Nelson; Chang, Zhan; Wishart, David S

    2004-04-12

    GelScape is a web-based tool that permits facile, interactive annotation, comparison, manipulation and storage of protein gel images. It uses Java applet-servlet technology to allow rapid, remote image handling and image processing in a platform-independent manner. It supports many of the features found in commercial, stand-alone gel analysis software including spot annotation, spot integration, gel warping, image resizing, HTML image mapping, image overlaying as well as the storage of gel image and gel annotation data in compliance with Federated Gel Database requirements.

  6. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  7. A UIMA wrapper for the NCBO annotator.

    Science.gov (United States)

    Roeder, Christophe; Jonquet, Clement; Shah, Nigam H; Baumgartner, William A; Verspoor, Karin; Hunter, Lawrence

    2010-07-15

    The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator-an ontology-based annotation service-to make it available as a component in UIMA workflows. This wrapper is freely available on the web at http://bionlp-uima.sourceforge.net/ as part of the UIMA tools distribution from the Center for Computational Pharmacology (CCP) at the University of Colorado School of Medicine. It has been implemented in Java for support on Mac OS X, Linux and MS Windows.

  8. Video tracking in the extreme: video analysis for nocturnal underwater animal movement.

    Science.gov (United States)

    Patullo, B W; Jolley-Rogers, G; Macmillan, D L

    2007-11-01

    Computer analysis of video footage is one option for recording locomotor behavior for a range of neurophysiological and behavioral studies. This technique is reasonably well established and accepted, but its use for some behavioral analyses remains a challenge. For example, filming through water can lead to reflection, and filming nocturnal activity can reduce resolution and clarity of filmed images. The aim of this study was to develop a noninvasive method for recording nocturnal activity in aquatic decapods and test the accuracy of analysis by video tracking software. We selected crayfish, Cherax destructor, because they are often active at night, they live underwater, and data on their locomotion is important for answering biological and physiological questions such as how they explore and navigate. We constructed recording arenas and filmed animals in infrared light. Wethen compared human observer data and software-acquired values. In this article, we outline important apparatus and software issues to obtain reliable computer tracking.

  9. Software system safety

    Science.gov (United States)

    Uber, James G.

    1988-01-01

    Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

  10. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

    Science.gov (United States)

    Duvick, Jon; Standage, Daniel S; Merchant, Nirav; Brendel, Volker P

    2016-04-01

    Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today's pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant's Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. © 2016 American Society of Plant Biologists. All rights reserved.

  11. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-08-01

    Full Text Available Abstract Background Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs. Results We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint™, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options. Conclusion POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in

  12. Enhanced Video Surveillance (EVS) with speckle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Carrano, C J

    2004-01-13

    Enhanced Video Surveillance (EVS) with Speckle Imaging is a high-resolution imaging system that substantially improves resolution and contrast in images acquired over long distances. This technology will increase image resolution up to an order of magnitude or greater for video surveillance systems. The system's hardware components are all commercially available and consist of a telescope or large-aperture lens assembly, a high-performance digital camera, and a personal computer. The system's software, developed at LLNL, extends standard speckle-image-processing methods (used in the astronomical community) to solve the atmospheric blurring problem associated with imaging over medium to long distances (hundreds of meters to tens of kilometers) through horizontal or slant-path turbulence. This novel imaging technology will not only enhance national security but also will benefit law enforcement, security contractors, and any private or public entity that uses video surveillance to protect their assets.

  13. Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

    OpenAIRE

    Kasukawa, Takeya; Furuno, Masaaki; Nikaido, Itoshi; Bono, Hidemasa; Hume, David A.; Bult, Carol; Hill, David P; Baldarelli, Richard; Gough, Julian; Kanapin, Alexander; Matsuda, Hideo; Schriml, Lynn M.; Hayashizaki, Yoshihide; Okazaki, Yasushi; Quackenbush, John

    2003-01-01

    Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools ...

  14. Recent advances in intelligent image search and video retrieval

    CERN Document Server

    2017-01-01

    This book initially reviews the major feature representation and extraction methods and effective learning and recognition approaches, which have broad applications in the context of intelligent image search and video retrieval. It subsequently presents novel methods, such as improved soft assignment coding, Inheritable Color Space (InCS) and the Generalized InCS framework, the sparse kernel manifold learner method, the efficient Support Vector Machine (eSVM), and the Scale-Invariant Feature Transform (SIFT) features in multiple color spaces. Lastly, the book presents clothing analysis for subject identification and retrieval, and performance evaluation methods of video analytics for traffic monitoring. Digital images and videos are proliferating at an amazing speed in the fields of science, engineering and technology, media and entertainment. With the huge accumulation of such data, keyword searches and manual annotation schemes may no longer be able to meet the practical demand for retrieving relevant conte...

  15. Automatic Story Segmentation for TV News Video Using Multiple Modalities

    Directory of Open Access Journals (Sweden)

    Émilie Dumont

    2012-01-01

    Full Text Available While video content is often stored in rather large files or broadcasted in continuous streams, users are often interested in retrieving only a particular passage on a topic of interest to them. It is, therefore, necessary to split video documents or streams into shorter segments corresponding to appropriate retrieval units. We propose here a method for the automatic segmentation of TV news videos into stories. A-multiple-descriptor based segmentation approach is proposed. The selected multimodal features are complementary and give good insights about story boundaries. Once extracted, these features are expanded with a local temporal context and combined by an early fusion process. The story boundaries are then predicted using machine learning techniques. We investigate the system by experiments conducted using TRECVID 2003 data and protocol of the story boundary detection task, and we show that the proposed approach outperforms the state-of-the-art methods while requiring a very small amount of manual annotation.

  16. REAL TIME SPEED ESTIMATION FROM MONOCULAR VIDEO

    Directory of Open Access Journals (Sweden)

    M. S. Temiz

    2012-07-01

    Full Text Available In this paper, detailed studies have been performed for developing a real time system to be used for surveillance of the traffic flow by using monocular video cameras to find speeds of the vehicles for secure travelling are presented. We assume that the studied road segment is planar and straight, the camera is tilted downward a bridge and the length of one line segment in the image is known. In order to estimate the speed of a moving vehicle from a video camera, rectification of video images is performed to eliminate the perspective effects and then the interest region namely the ROI is determined for tracking the vehicles. Velocity vectors of a sufficient number of reference points are identified on the image of the vehicle from each video frame. For this purpose sufficient number of points from the vehicle is selected, and these points must be accurately tracked on at least two successive video frames. In the second step, by using the displacement vectors of the tracked points and passed time, the velocity vectors of those points are computed. Computed velocity vectors are defined in the video image coordinate system and displacement vectors are measured by the means of pixel units. Then the magnitudes of the computed vectors in the image space are transformed to the object space to find the absolute values of these magnitudes. The accuracy of the estimated speed is approximately ±1 – 2 km/h. In order to solve the real time speed estimation problem, the authors have written a software system in C++ programming language. This software system has been used for all of the computations and test applications.

  17. Understanding Video Games

    DEFF Research Database (Denmark)

    Heide Smith, Jonas; Tosca, Susana Pajares; Egenfeldt-Nielsen, Simon

    From Pong to PlayStation 3 and beyond, Understanding Video Games is the first general introduction to the exciting new field of video game studies. This textbook traces the history of video games, introduces the major theories used to analyze games such as ludology and narratology, reviews...... the economics of the game industry, examines the aesthetics of game design, surveys the broad range of game genres, explores player culture, and addresses the major debates surrounding the medium, from educational benefits to the effects of violence. Throughout the book, the authors ask readers to consider...... larger questions about the medium: * What defines a video game? * Who plays games? * Why do we play games? * How do games affect the player? Extensively illustrated, Understanding Video Games is an indispensable and comprehensive resource for those interested in the ways video games are reshaping...

  18. Collaborative Video Sketching

    DEFF Research Database (Denmark)

    Henningsen, Birgitte; Gundersen, Peter Bukovica; Hautopp, Heidi

    2017-01-01

    This paper introduces to what we define as a collaborative video sketching process. This process links various sketching techniques with digital storytelling approaches and creative reflection processes in video productions. Traditionally, sketching has been used by designers across various...... forms and through empirical examples, we present and discuss the video recording of sketching sessions, as well as development of video sketches by rethinking, redoing and editing the recorded sessions. The empirical data is based on workshop sessions with researchers and students from universities...... and university colleges and primary and secondary school teachers. As researchers, we have had different roles in these action research case studies where various video sketching techniques were applied.The analysis illustrates that video sketching can take many forms, and two common features are important...

  19. Reflections on academic video

    Directory of Open Access Journals (Sweden)

    Thommy Eriksson

    2012-11-01

    Full Text Available As academics we study, research and teach audiovisual media, yet rarely disseminate and mediate through it. Today, developments in production technologies have enabled academic researchers to create videos and mediate audiovisually. In academia it is taken for granted that everyone can write a text. Is it now time to assume that everyone can make a video essay? Using the online journal of academic videos Audiovisual Thinking and the videos published in it as a case study, this article seeks to reflect on the emergence and legacy of academic audiovisual dissemination. Anchoring academic video and audiovisual dissemination of knowledge in two critical traditions, documentary theory and semiotics, we will argue that academic video is in fact already present in a variety of academic disciplines, and that academic audiovisual essays are bringing trends and developments that have long been part of academic discourse to their logical conclusion.

  20. Ranking Biomedical Annotations with Annotator’s Semantic Relevancy

    Directory of Open Access Journals (Sweden)

    Aihua Wu

    2014-01-01

    Full Text Available Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator’s knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user’s vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large.

  1. Educational video recording and editing for the hand surgeon.

    Science.gov (United States)

    Rehim, Shady A; Chung, Kevin C

    2015-05-01

    Digital video recordings are increasingly used across various medical and surgical disciplines including hand surgery for documentation of patient care, resident education, scientific presentations, and publications. In recent years, the introduction of sophisticated computer hardware and software technology has simplified the process of digital video production and improved means of disseminating large digital data files. However, the creation of high-quality surgical video footage requires a basic understanding of key technical considerations, together with creativity and sound aesthetic judgment of the videographer. In this article we outline the practical steps involved in equipment preparation, video recording, editing, and archiving, as well as guidance for the choice of suitable hardware and software equipment. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  2. Making Sure What You See Is What You Get: Digital Video Technology and the Preparation of Teachers of Elementary Science

    Science.gov (United States)

    Bueno de Mesquita, Paul; Dean, Ross F.; Young, Betty J.

    2010-01-01

    Advances in digital video technology create opportunities for more detailed qualitative analyses of actual teaching practice in science and other subject areas. User-friendly digital cameras and highly developed, flexible video-analysis software programs have made the tasks of video capture, editing, transcription, and subsequent data analysis…

  3. NASA Software Engineering Benchmarking Study

    Science.gov (United States)

    Rarick, Heather L.; Godfrey, Sara H.; Kelly, John C.; Crumbley, Robert T.; Wifl, Joel M.

    2013-01-01

    .onsolidate, collect and, if needed, develop common processes principles and other assets across the Agency in order to provide more consistency in software development and acquisition practices and to reduce the overall cost of maintaining or increasing current NASA CMMI maturity levels. 6. Provide additional support for small projects that includes: (a) guidance for appropriate tailoring of requirements for small projects, (b) availability of suitable tools, including support tool set-up and training, and (c) training for small project personnel, assurance personnel and technical authorities on the acceptable options for tailoring requirements and performing assurance on small projects. 7. Develop software training classes for the more experienced software engineers using on-line training, videos, or small separate modules of training that can be accommodated as needed throughout a project. 8. Create guidelines to structure non-classroom training opportunities such as mentoring, peer reviews, lessons learned sessions, and on-the-job training. 9. Develop a set of predictive software defect data and a process for assessing software testing metric data against it. 10. Assess Agency-wide licenses for commonly used software tools. 11. Fill the knowledge gap in common software engineering practices for new hires and co-ops.12. Work through the Science, Technology, Engineering and Mathematics (STEM) program with universities in strengthening education in the use of common software engineering practices and standards. 13. Follow up this benchmark study with a deeper look into what both internal and external organizations perceive as the scope of software assurance, the value they expect to obtain from it, and the shortcomings they experience in the current practice. 14. Continue interactions with external software engineering environment through collaborations, knowledge sharing, and benchmarking.

  4. Mulligan Concept manual therapy: standardizing annotation.

    Science.gov (United States)

    McDowell, Jillian Marie; Johnson, Gillian Margaret; Hetherington, Barbara Helen

    2014-10-01

    Quality technique documentation is integral to the practice of manual therapy, ensuring uniform application and reproducibility of treatment. Manual therapy techniques are described by annotations utilizing a range of acronyms, abbreviations and universal terminology based on biomechanical and anatomical concepts. The various combinations of therapist and patient generated forces utilized in a variety of weight-bearing positions, which are synonymous with Mulligan Concept, challenge practitioners existing annotational skills. An annotation framework with recording rules adapted to the Mulligan Concept is proposed in which the abbreviations incorporate established manual therapy tenets and are detailed in the following sequence of; starting position, side, joint/s, method of application, glide/s, Mulligan technique, movement (or function), whether an assistant is used, overpressure (and by whom) and numbers of repetitions or time and sets. Therapist or patient application of overpressure and utilization of treatment belts or manual techniques must be recorded to capture the complete description. The adoption of the Mulligan Concept annotation framework in this way for documentation purposes will provide uniformity and clarity of information transfer for the future purposes of teaching, clinical practice and audit for its practitioners. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Metric Conversion: An Annotated Bibliography for Teachers.

    Science.gov (United States)

    National Education Association, Washington, DC.

    This annotated bibliography was compiled to provide teachers with sources of information concerning the metric system. Articles of general interest concerning the reasons for change and experiences of others in implementing the change are included, as well as materials for practical use by teachers. Books and articles from current journals are…

  6. Annotating State of Mind in Meeting Data

    NARCIS (Netherlands)

    Heylen, Dirk K.J.; Reidsma, Dennis; Ordelman, Roeland J.F.; Devillers, L.; Martin, J-C.; Cowie, R.; Batliner, A.

    We discuss the annotation procedure for mental state and emotion that is under development for the AMI (Augmented Multiparty Interaction) corpus. The categories that were found to be most appropriate relate not only to emotions but also to (meta-)cognitive states and interpersonal variables. The

  7. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  8. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  9. ePNK Applications and Annotations

    DEFF Research Database (Denmark)

    Kindler, Ekkart

    2017-01-01

    newapplicationsfor the ePNK and, in particular, visualizing the result of an application in the graphical editor of the ePNK by singannotations, and interacting with the end user using these annotations. In this paper, we give an overview of the concepts of ePNK applications by discussing the implementation...

  10. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  11. La Mujer Chicana: An Annotated Bibliography, 1976.

    Science.gov (United States)

    Chapa, Evey, Ed.; And Others

    Intended to provide interested persons, researchers, and educators with information about "la mujer Chicana", this annotated bibliography cites 320 materials published between 1916 and 1975, with the majority being between 1960 and 1975. The 12 sections cover the following subject areas: Chicana publications; Chicana feminism and…

  12. Bibliografia de Aztlan: An Annotated Chicano Bibliography.

    Science.gov (United States)

    Barrios, Ernie, Ed.

    More than 300 books and articles published from 1920 to 1971 are reviewed in this annotated bibliography of literature on the Chicano. The citations and reviews are categorized by subject area and deal with contemporary Chicano history, education, health, history of Mexico, literature, native Americans, philosophy, political science, pre-Columbian…

  13. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  14. College Students in Transition: An Annotated Bibliography

    Science.gov (United States)

    Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

    2013-01-01

    The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

  15. Structuring and presenting annotated media repositories

    NARCIS (Netherlands)

    L. Rutledge (Lloyd); J.R. van Ossenbruggen (Jacco); L. Hardman (Lynda)

    2004-01-01

    textabstractThe Semantic Web envisions a Web that is both human readable and machine processible. In practice, however, there is still a large conceptual gap between annotated content repositories on the one hand, and coherent, human readable Web pages on the other. To bridge this conceptual gap,

  16. Learning to search for images without annotations

    NARCIS (Netherlands)

    Kordumova, S.

    2016-01-01

    Humans are adjusted to the environment and can easily recognize what they see around them or in images. Machines, however, cannot recognize images unless trained to do so. The usual approach is to annotate images with what they capture and train a machine learning algorithm. This thesis focuses on a

  17. Just-in-time : on strategy annotations

    NARCIS (Netherlands)

    J.C. van de Pol (Jaco)

    2001-01-01

    textabstractA simple kind of strategy annotations is investigated, giving rise to a class of strategies, including leftmost-innermost. It is shown that under certain restrictions, an interpreter can be written which computes the normal form of a term in a bottom-up traversal. The main contribution

  18. Great Basin Experimental Range: Annotated bibliography

    Science.gov (United States)

    E. Durant McArthur; Bryce A. Richardson; Stanley G. Kitchen

    2013-01-01

    This annotated bibliography documents the research that has been conducted on the Great Basin Experimental Range (GBER, also known as the Utah Experiment Station, Great Basin Station, the Great Basin Branch Experiment Station, Great Basin Experimental Center, and other similar name variants) over the 102 years of its existence. Entries were drawn from the original...

  19. Nutrition & Adolescent Pregnancy: A Selected Annotated Bibliography.

    Science.gov (United States)

    National Agricultural Library (USDA), Washington, DC.

    This annotated bibliography on nutrition and adolescent pregnancy is intended to be a source of technical assistance for nurses, nutritionists, physicians, educators, social workers, and other personnel concerned with improving the health of teenage mothers and their babies. It is divided into two major sections. The first section lists selected…

  20. Georgia Journalism: A Selected, Annotated Bibliography.

    Science.gov (United States)

    Eberhard, Wallace B.; Bickers, Christopher E.

    Assembled as a preliminary list of publications concerning Georgia journalism, this selected, annotated bibliography is intended to be useful to secondary teachers interested in history and journalism, to be helpful to students and scholars of mass media, and to indicate some obvious gaps in the literature of journalism as it pertains to the state…

  1. Snap: An Integrated SNP Annotation Platform

    DEFF Research Database (Denmark)

    Li, S.; Ma, L.; Li, H.

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

  2. Locating Educational Facilities. An Annotated Reference List.

    Science.gov (United States)

    Wakefield, Howard E.

    An annotated reference list of documents received and processed by the ERIC Clearinghouse on Educational Facilities. These documents are concerned wholly or partially with school and facilities location and site selection. All levels of education are covered and each document i s indexed and abstracted. (NI)

  3. Scalable gastroscopic video summarization via similar-inhibition dictionary selection.

    Science.gov (United States)

    Wang, Shuai; Cong, Yang; Cao, Jun; Yang, Yunsheng; Tang, Yandong; Zhao, Huaici; Yu, Haibin

    2016-01-01

    This paper aims at developing an automated gastroscopic video summarization algorithm to assist clinicians to more effectively go through the abnormal contents of the video. To select the most representative frames from the original video sequence, we formulate the problem of gastroscopic video summarization as a dictionary selection issue. Different from the traditional dictionary selection methods, which take into account only the number and reconstruction ability of selected key frames, our model introduces the similar-inhibition constraint to reinforce the diversity of selected key frames. We calculate the attention cost by merging both gaze and content change into a prior cue to help select the frames with more high-level semantic information. Moreover, we adopt an image quality evaluation process to eliminate the interference of the poor quality images and a segmentation process to reduce the computational complexity. For experiments, we build a new gastroscopic video dataset captured from 30 volunteers with more than 400k images and compare our method with the state-of-the-arts using the content consistency, index consistency and content-index consistency with the ground truth. Compared with all competitors, our method obtains the best results in 23 of 30 videos evaluated based on content consistency, 24 of 30 videos evaluated based on index consistency and all videos evaluated based on content-index consistency. For gastroscopic video summarization, we propose an automated annotation method via similar-inhibition dictionary selection. Our model can achieve better performance compared with other state-of-the-art models and supplies more suitable key frames for diagnosis. The developed algorithm can be automatically adapted to various real applications, such as the training of young clinicians, computer-aided diagnosis or medical report generation. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Sound for digital video

    CERN Document Server

    Holman, Tomlinson

    2013-01-01

    Achieve professional quality sound on a limited budget! Harness all new, Hollywood style audio techniques to bring your independent film and video productions to the next level.In Sound for Digital Video, Second Edition industry experts Tomlinson Holman and Arthur Baum give you the tools and knowledge to apply recent advances in audio capture, video recording, editing workflow, and mixing to your own film or video with stunning results. This fresh edition is chockfull of techniques, tricks, and workflow secrets that you can apply to your own projects from preproduction

  5. Green Power Partnership Videos

    Science.gov (United States)

    The Green Power Partnership develops videos on a regular basis that explore a variety of topics including, Green Power partnership, green power purchasing, Renewable energy certificates, among others.

  6. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  7. A novel video dataset for change detection benchmarking.

    Science.gov (United States)

    Goyette, Nil; Jodoin, Pierre-Marc; Porikli, Fatih; Konrad, Janusz; Ishwar, Prakash

    2014-11-01

    Change detection is one of the most commonly encountered low-level tasks in computer vision and video processing. A plethora of algorithms have been developed to date, yet no widely accepted, realistic, large-scale video data set exists for benchmarking different methods. Presented here is a unique change detection video data set consisting of nearly 90 000 frames in 31 video sequences representing six categories selected to cover a wide range of challenges in two modalities (color and thermal infrared). A distinguishing characteristic of this benchmark video data set is that each frame is meticulously annotated by hand for ground-truth foreground, background, and shadow area boundaries-an effort that goes much beyond a simple binary label denoting the presence of change. This enables objective and precise quantitative comparison and ranking of video-based change detection algorithms. This paper discusses various aspects of the new data set, quantitative performance metrics used, and comparative results for over two dozen change detection algorithms. It draws important conclusions on solved and remaining issues in change detection, and describes future challenges for the scientific community. The data set, evaluation tools, and algorithm rankings are available to the public on a website and will be updated with feedback from academia and industry in the future.

  8. The TIGR Rice Genome Annotation Resource: improvements and new features

    National Research Council Canada - National Science Library

    Ouyang, Shu; Zhu, Wei; Hamilton, John; Lin, Haining; Campbell, Matthew; Childs, Kevin; Thibaud-Nissen, Françoise; Malek, Renae L; Lee, Yuandan; Zheng, Li; Orvis, Joshua; Haas, Brian; Wortman, Jennifer; Buell, C Robin

    2007-01-01

    In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation...

  9. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  10. Annotation Method (AM): SE22_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Comparison with public data...bases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...

  11. Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge.

    Science.gov (United States)

    Kassahn, Karin S; Scott, Hamish S; Caramins, Melody C

    2014-04-01

    Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardized variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer. © 2014 WILEY PERIODICALS, INC.

  12. Sandia software guidelines: Software quality planning

    Energy Technology Data Exchange (ETDEWEB)

    1987-08-01

    This volume is one in a series of Sandia Software Guidelines intended for use in producing quality software within Sandia National Laboratories. In consonance with the IEEE Standard for Software Quality Assurance Plans, this volume identifies procedures to follow in producing a Software Quality Assurance Plan for an organization or a project, and provides an example project SQA plan. 2 figs., 4 tabs.

  13. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

    OpenAIRE

    Qiandong Zeng; William Klimke; Peter Sterk; Susmita Shrivastava; Ramana Madupu; Scheuermann, Richard H.; Seth Schobel; Donald Seto; Yiming Bao; Carla Kuiken; Lefkowitz, Elliot J.; Philippe Le Mercier; Raphael Leplae; Tatiana Tatusova; James Rodney Brister

    2010-01-01

    Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing...

  14. Representing annotation compositionality and provenance for the Semantic Web.

    Science.gov (United States)

    Livingston, Kevin M; Bada, Michael; Hunter, Lawrence E; Verspoor, Karin

    2013-01-01

    Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures formally defined in terms of more atomic knowledge structures. Existing provenance efforts in the Semantic Web domain primarily focus on tracking provenance at the level of whole triples and do not provide enough detail to track how individual triple elements of annotations were derived from triple elements of other annotations. We present a task- and domain-independent ontological model for capturing annotations and their linkage to their denoted knowledge representations, which can be singular concepts or more complex sets of assertions. We have implemented this model as an extension of the Information Artifact Ontology in OWL and made it freely available, and we show how it can be integrated with several prominent annotation and provenance models. We present several application areas for the model, ranging from linguistic annotation of text to the annotation of disease-associations in genome sequences. With this model, progressively more complex annotations can be composed from other annotations, and the provenance of compositional annotations can be represented at the annotation level or at the level of individual elements of the RDF triples composing the annotations. This in turn allows for progressively richer annotations to be constructed from previous annotation efforts, the precise provenance recording of which facilitates evidence-based inference and error tracking.

  15. BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

    Science.gov (United States)

    Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

    2015-08-18

    Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  16. AnnaBot: A Static Verifier for Java Annotation Usage

    OpenAIRE

    Ian Darwin

    2010-01-01

    This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in ...

  17. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  18. Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies.

    Science.gov (United States)

    Koch, Lisa M; Rajchl, Martin; Bai, Wenjia; Baumgartner, Christian F; Tong, Tong; Passerat-Palmbach, Jonathan; Aljabar, Paul; Rueckert, Daniel

    2017-08-22

    Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation.

  19. Content and ratings of mature-rated video games.

    Science.gov (United States)

    Thompson, Kimberly M; Tepichin, Karen; Haninger, Kevin

    2006-04-01

    To quantify the depiction of violence, blood, sexual themes, profanity, substances, and gambling in video games rated M (for "mature") and to measure agreement between the content observed and the rating information provided to consumers on the game box by the Entertainment Software Rating Board. We created a database of M-rated video game titles, selected a random sample, recorded at least 1 hour of game play, quantitatively assessed the content, performed statistical analyses to describe the content, and compared our observations with the Entertainment Software Rating Board content descriptors and results of our prior studies. Harvard University, Boston, Mass. Authors and 1 hired game player. M-rated video games. Percentages of game play depicting violence, blood, sexual themes, gambling, alcohol, tobacco, or other drugs; use of profanity in dialogue, song lyrics, or gestures. Although the Entertainment Software Rating Board content descriptors for violence and blood provide a good indication of such content in the game, we identified 45 observations of content that could warrant a content descriptor in 29 games (81%) that lacked these content descriptors. M-rated video games are significantly more likely to contain blood, profanity, and substances; depict more severe injuries to human and nonhuman characters; and have a higher rate of human deaths than video games rated T (for "teen"). Parents and physicians should recognize that popular M-rated video games contain a wide range of unlabeled content and may expose children and adolescents to messages that may negatively influence their perceptions, attitudes, and behaviors.

  20. Software engineering architecture-driven software development

    CERN Document Server

    Schmidt, Richard F

    2013-01-01

    Software Engineering: Architecture-driven Software Development is the first comprehensive guide to the underlying skills embodied in the IEEE's Software Engineering Body of Knowledge (SWEBOK) standard. Standards expert Richard Schmidt explains the traditional software engineering practices recognized for developing projects for government or corporate systems. Software engineering education often lacks standardization, with many institutions focusing on implementation rather than design as it impacts product architecture. Many graduates join the workforce with incomplete skil

  1. THE RESEARCH ON PROGRAMED INSTRUCTION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    SCHRAMM, WILBUR

    AN ANNOTATED BIBLIOGRAPHY AND DISCUSSION OF THE RESEARCH ON PROGRAMED INSTRUCTION CONDUCTED SINCE 1954 HAS BEEN PREPARED. FOLLOWING AN INTRODUCTION BY THE AUTHOR, OVER 200 ANNOTATIONS WERE PRESENTED, ALPHABETICALLY BY SENIOR AUTHORS. THE ANNOTATIONS ARE DETAILED AND INFORMATIVE, AND WERE SUBMITTED TO THEIR AUTHORS FOR CHECKING. (JC)

  2. GRaSP: A Multilayered Annotation Scheme for Perspectives

    NARCIS (Netherlands)

    van Son, C.M.; Caselli, T.; Fokkens, A.S.; Maks, E.; Morante Vallejo, R.; Aroyo, L.M.; Vossen, P.T.J.M.

    2016-01-01

    This paper presents a framework and methodology for the annotation of perspectives in text. In the last decade, different aspects of linguistic encoding of perspectives have been targeted as separated phenomena through different annotation initiatives. We propose an annotation scheme that integrates

  3. FPGA Implementation of Video Transmission System Based on LTE

    Directory of Open Access Journals (Sweden)

    Lu Yan

    2015-01-01

    Full Text Available In order to support high-definition video transmission, an implementation of video transmission system based on Long Term Evolution is designed. This system is developed on Xilinx Virtex-6 FPGA ML605 Evaluation Board. The paper elaborates the features of baseband link designed in Xilinx ISE and protocol stack designed in Xilinx SDK, and introduces the process of setting up hardware and software platform in Xilinx XPS. According to test, this system consumes less hardware resource and is able to transmit bidirectional video clearly and stably.

  4. Functional annotation of the human retinal pigment epithelium transcriptome

    Directory of Open Access Journals (Sweden)

    Gorgels Theo GMF

    2009-04-01

    Full Text Available Abstract Background To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE, the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy human donor eyes (aged 63–78 years were laser dissected and used for 22k microarray studies (Agilent technologies. Data were analyzed with Rosetta Resolver, the web tool DAVID and Ingenuity software. Results In total, we identified 19,746 array entries with significant expression in the RPE. Gene expression was analyzed according to expression levels, interindividual variability and functionality. A group of highly (n = 2,194 expressed RPE genes showed an overrepresentation of genes of the oxidative phosphorylation, ATP synthesis and ribosome pathways. In the group of moderately expressed genes (n = 8,776 genes of the phosphatidylinositol signaling system and aminosugars metabolism were overrepresented. As expected, the top 10 percent (n = 2,194 of genes with the highest interindividual differences in expression showed functional overrepresentation of the complement cascade, essential in inflammation in age-related macular degeneration, and other signaling pathways. Surprisingly, this same category also includes the genes involved in Bruch's membrane (BM composition. Among the top 10 percent of genes with low interindividual differences, there was an overrepresentation of genes involved in local glycosaminoglycan turnover. Conclusion Our study expands current knowledge of the RPE transcriptome by assigning new genes, and adding data about expression level and interindividual variation. Functional annotation suggests that the RPE has high levels of protein synthesis, strong energy demands, and is exposed to high levels of oxidative stress and a variable degree of inflammation. Our data sheds new light on the molecular composition of BM, adjacent to the

  5. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... a Group Upcoming Events Video Library Photo Gallery One-on-One Support ANetwork Peer Support Program Community Connections Overview ... group Back Upcoming events Video Library Photo Gallery One-on-One Support Back ANetwork Peer Support Program ...

  6. AudioMove Video

    DEFF Research Database (Denmark)

    2012-01-01

    Live drawing video experimenting with low tech techniques in the field of sketching and visual sense making. In collaboration with Rune Wehner and Teater Katapult.......Live drawing video experimenting with low tech techniques in the field of sketching and visual sense making. In collaboration with Rune Wehner and Teater Katapult....

  7. Making Good Physics Videos

    Science.gov (United States)

    Lincoln, James

    2017-01-01

    Online videos are an increasingly important way technology is contributing to the improvement of physics teaching. Students and teachers have begun to rely on online videos to provide them with content knowledge and instructional strategies. Online audiences are expecting greater production value, and departments are sometimes requesting educators…

  8. SECRETS OF SONG VIDEO

    Directory of Open Access Journals (Sweden)

    Chernyshov Alexander V.

    2014-04-01

    Full Text Available The article focuses on the origins of the song videos as TV and Internet-genre. In addition, it considers problems of screen images creation depending on the musical form and the text of a songs in connection with relevant principles of accent and phraseological video editing and filming techniques as well as with additional frames and sound elements.

  9. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... support group for me? Find a Group Upcoming Events Video Library Photo Gallery One-on-One Support ANetwork Peer ... group for me? Find a group Back Upcoming events Video Library Photo Gallery One-on-One Support Back ANetwork ...

  10. Personal Digital Video Stories

    DEFF Research Database (Denmark)

    Ørngreen, Rikke; Henningsen, Birgitte Sølbeck; Louw, Arnt Vestergaard

    2016-01-01

    agenda focusing on video productions in combination with digital storytelling, followed by a presentation of the digital storytelling features. The paper concludes with a suggestion to initiate research in what is identified as Personal Digital Video (PDV) Stories within longitudinal settings, while...

  11. The Video Generation.

    Science.gov (United States)

    Provenzo, Eugene F., Jr.

    1992-01-01

    Video games are neither neutral nor harmless but represent very specific social and symbolic constructs. Research on the social content of today's video games reveals that sex bias and gender stereotyping are widely evident throughout the Nintendo games. Violence and aggression also pervade the great majority of the games. (MLF)

  12. Guest Editorial: Analysis and Retrieval of Events/Actions and Workflows in Video Streams

    DEFF Research Database (Denmark)

    Doulamis, Anastasios; Doulamis, Nikolaos; Bertini, Marco

    2016-01-01

    Cognitive video supervision and event analysis in video sequences is a critical task in many multimedia applications. Methods, tools, and algorithms that aim to detect and recognize high-level concepts and their respective spatiotemporal and causal relations in order to identify semantic video...... activities, actions, and procedures have been in the focus of the research community over the last years. This research area has strong impact on many real-life applications such as service quality assurance, compliance to the designed procedures in industrial plants, surveillance of people-dense areas (e.......g., thematic parks, critical public infrastructures), crisis management in public service areas (e.g., train stations, airports), security (detection of abnormal behaviors in surveillance videos), semantic characterization, and annotation of video streams in various domains (e.g., broadcast or user...

  13. Rheumatoid Arthritis Educational Video Series

    Medline Plus

    Full Text Available ... Patient Webcasts / Rheumatoid Arthritis Educational Video Series Rheumatoid Arthritis Educational Video Series This series of five videos ... member of our patient care team. Managing Your Arthritis Managing Your Arthritis Managing Chronic Pain and Depression ...

  14. Rheumatoid Arthritis Educational Video Series

    Medline Plus

    Full Text Available ... Corner / Patient Webcasts / Rheumatoid Arthritis Educational Video Series Rheumatoid Arthritis Educational Video Series This series of five videos was designed to help you learn more about Rheumatoid Arthritis (RA). You will learn how the diagnosis of ...

  15. Rheumatoid Arthritis Educational Video Series

    Science.gov (United States)

    ... Corner / Patient Webcasts / Rheumatoid Arthritis Educational Video Series Rheumatoid Arthritis Educational Video Series This series of five videos was designed to help you learn more about Rheumatoid Arthritis (RA). You will learn how the diagnosis of ...

  16. NEI You Tube Videos: Amblyopia

    Medline Plus

    Full Text Available ... questions Clinical Studies Publications Catalog Photos and Images Spanish Language Information Grants and Funding Extramural Research Division ... Low Vision Refractive Errors Retinopathy of Prematurity Science Spanish Videos Webinars NEI YouTube Videos: Amblyopia Embedded video ...

  17. Social video content delivery

    CERN Document Server

    Wang, Zhi; Zhu, Wenwu

    2016-01-01

    This brief presents new architecture and strategies for distribution of social video content. A primary framework for socially-aware video delivery and a thorough overview of the possible approaches is provided. The book identifies the unique characteristics of socially-aware video access and social content propagation, revealing the design and integration of individual modules that are aimed at enhancing user experience in the social network context. The change in video content generation, propagation, and consumption for online social networks, has significantly challenged the traditional video delivery paradigm. Given the massive amount of user-generated content shared in online social networks, users are now engaged as active participants in the social ecosystem rather than as passive receivers of media content. This revolution is being driven further by the deep penetration of 3G/4G wireless networks and smart mobile devices that are seamlessly integrated with online social networking and media-sharing s...

  18. Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

    Science.gov (United States)

    Jupp, Simon; Stevens, Robert; Hoehndorf, Robert

    2012-04-24

    Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations of gene products that can be exploited in query and analysis. As many annotations with different ontologies centre upon gene products, there is a possibility to explore gene products through multiple ontological perspectives at the same time. Questions could be asked that link a gene product's function, process, cellular location, phenotype and disease. Current tools, such as AmiGO, allow exploration of genes based on their GO annotations, but not through multiple ontological perspectives. In addition, the semantics of these ontology's representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible. To do this multi-perspective, richer querying of gene product annotations, we have created the Logical Gene Ontology, or GOAL ontology, in OWL that combines the Gene Ontology, Human Disease Ontology and the Mammalian Phenotype Ontology, together with classes that represent the annotations with these ontologies for mouse gene products. Each mouse gene product is represented as a class, with the appropriate relationships to the GO aspects, phenotype and disease with which it has been annotated. We then use defined classes to query these protein classes through automated reasoning, and to build a complex hierarchy of gene products. We have presented this through a Web interface that allows arbitrary queries to be constructed and the results displayed. This standard use of OWL affords a rich interaction with Gene Ontology, Human Disease Ontology and Mammalian Phenotype Ontology annotations for the mouse, to give a fine partitioning of

  19. The software life cycle

    CERN Document Server

    Ince, Darrel

    1990-01-01

    The Software Life Cycle deals with the software lifecycle, that is, what exactly happens when software is developed. Topics covered include aspects of software engineering, structured techniques of software development, and software project management. The use of mathematics to design and develop computer systems is also discussed. This book is comprised of 20 chapters divided into four sections and begins with an overview of software engineering and software development, paying particular attention to the birth of software engineering and the introduction of formal methods of software develop

  20. Authentication of digital video evidence

    Science.gov (United States)

    Beser, Nicholas D.; Duerr, Thomas E.; Staisiunas, Gregory P.

    2003-11-01

    In response to a requirement from the United States Postal Inspection Service, the Technical Support Working Group tasked The Johns Hopkins University Applied Physics Laboratory (JHU/APL) to develop a technique tha will ensure the authenticity, or integrity, of digital video (DV). Verifiable integrity is needed if DV evidence is to withstand a challenge to its admissibility in court on the grounds that it can be easily edited. Specifically, the verification technique must detect additions, deletions, or modifications to DV and satisfy the two-part criteria pertaining to scientific evidence as articulated in Daubert et al. v. Merrell Dow Pharmaceuticals Inc., 43 F3d (9th Circuit, 1995). JHU/APL has developed a prototype digital video authenticator (DVA) that generates digital signatures based on public key cryptography at the frame level of the DV. Signature generation and recording is accomplished at the same time as DV is recorded by the camcorder. Throughput supports the consumer-grade camcorder data rate of 25 Mbps. The DVA software is implemented on a commercial laptop computer, which is connected to a commercial digital camcorder via the IEEE-1394 serial interface. A security token provides agent identification and the interface to the public key infrastructure (PKI) that is needed for management of the public keys central to DV integrity verification.

  1. Violence in Teen-Rated Video Games

    Science.gov (United States)

    Haninger, Kevin; Ryan, M. Seamus; Thompson, Kimberly M

    2004-01-01

    Context: Children's exposure to violence in the media remains a source of public health concern; however, violence in video games rated T (for “Teen”) by the Entertainment Software Rating Board (ESRB) has not been quantified. Objective: To quantify and characterize the depiction of violence and blood in T-rated video games. According to the ESRB, T-rated video games may be suitable for persons aged 13 years and older and may contain violence, mild or strong language, and/or suggestive themes. Design: We created a database of all 396 T-rated video game titles released on the major video game consoles in the United States by April 1, 2001 to identify the distribution of games by genre and to characterize the distribution of content descriptors for violence and blood assigned to these games. We randomly sampled 80 game titles (which included 81 games because 1 title included 2 separate games), played each game for at least 1 hour, and quantitatively assessed the content. Given the release of 2 new video game consoles, Microsoft Xbox and Nintendo GameCube, and a significant number of T-rated video games released after we drew our random sample, we played and assessed 9 additional games for these consoles. Finally, we assessed the content of 2 R-rated films, The Matrix and The Matrix: Reloaded, associated with the T-rated video game Enter the Matrix. Main Outcome Measures: Game genre; percentage of game play depicting violence; depiction of injury; depiction of blood; number of human and nonhuman fatalities; types of weapons used; whether injuring characters, killing characters, or destroying objects is rewarded or is required to advance in the game; and content that may raise concerns about marketing T-rated video games to children. Results: Based on analysis of the 396 T-rated video game titles, 93 game titles (23%) received content descriptors for both violence and blood, 280 game titles (71%) received only a content descriptor for violence, 9 game titles (2

  2. Violence in teen-rated video games.

    Science.gov (United States)

    Haninger, Kevin; Ryan, M Seamus; Thompson, Kimberly M

    2004-03-11

    Children's exposure to violence in the media remains a source of public health concern; however, violence in video games rated T (for "Teen") by the Entertainment Software Rating Board (ESRB) has not been quantified. To quantify and characterize the depiction of violence and blood in T-rated video games. According to the ESRB, T-rated video games may be suitable for persons aged 13 years and older and may contain violence, mild or strong language, and/or suggestive themes. We created a database of all 396 T-rated video game titles released on the major video game consoles in the United States by April 1, 2001 to identify the distribution of games by genre and to characterize the distribution of content descriptors for violence and blood assigned to these games. We randomly sampled 80 game titles (which included 81 games because 1 title included 2 separate games), played each game for at least 1 hour, and quantitatively assessed the content. Given the release of 2 new video game consoles, Microsoft Xbox and Nintendo GameCube, and a significant number of T-rated video games released after we drew our random sample, we played and assessed 9 additional games for these consoles. Finally, we assessed the content of 2 R-rated films, The Matrix and The Matrix: Reloaded, associated with the T-rated video game Enter the Matrix. Game genre; percentage of game play depicting violence; depiction of injury; depiction of blood; number of human and nonhuman fatalities; types of weapons used; whether injuring characters, killing characters, or destroying objects is rewarded or is required to advance in the game; and content that may raise concerns about marketing T-rated video games to children. Based on analysis of the 396 T-rated video game titles, 93 game titles (23%) received content descriptors for both violence and blood, 280 game titles (71%) received only a content descriptor for violence, 9 game titles (2%) received only a content descriptor for blood, and 14 game titles

  3. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

    Science.gov (United States)

    Ghaffari, Noushin; Sanchez-Flores, Alejandro; Doan, Ryan; Garcia-Orozco, Karina D.; Chen, Patricia L.; Ochoa-Leyva, Adrian; Lopez-Zavala, Alonso A.; Carrasco, J. Salvador; Hong, Chris; Brieba, Luis G.; Rudiño-Piñera, Enrique; Blood, Philip D.; Sawyer, Jason E.; Johnson, Charles D.; Dindot, Scott V.; Sotelo-Mundo, Rogerio R.; Criscitiello, Michael F.

    2014-01-01

    We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod Daphnia allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance. PMID:25420880

  4. Analysis and Annotation of Nucleic Acid Sequence

    Energy Technology Data Exchange (ETDEWEB)

    David J. States

    1998-08-01

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  5. Software fault tolerance

    OpenAIRE

    Kazinov, Tofik Hasanaga; Mostafa, Jalilian Shahrukh

    2009-01-01

    Because of our present inability to produce errorfree software, software fault tolerance is and will contiune to be an important consideration in software system. The root cause of software design errors in the complexity of the systems. This paper surveys various software fault tolerance techniquest and methodologies. They are two gpoups: Single version and Multi version software fault tolerance techniques. It is expected that software fault tolerance research will benefit from this research...

  6. Three-dimensional video presentation of microsurgery by the cross-eyed viewing method using a high-definition video system.

    Science.gov (United States)

    Terakawa, Yuzo; Ishibashi, Kenichi; Goto, Takeo; Ohata, Kenji

    2011-01-01

    Three-dimensional (3-D) video recording of microsurgery is a more promising tool for presentation and education of microsurgery than conventional two-dimensional video systems, but has not been widely adopted partly because 3-D image processing of previous 3-D video systems is complicated and observers without optical devices cannot visualize the 3-D image. A new technical development for 3-D video presentation of microsurgery is described. Microsurgery is recorded with a microscope equipped with a single high-definition (HD) video camera. This 3-D video system records the right- and left-eye views of the microscope simultaneously as single HD data with the use of a 3-D camera adapter: the right- and left-eye views of the microscope are displayed separately on the right and left sides, respectively. The operation video is then edited with video editing software so that the right-eye view is displayed on the left side and left-eye view is displayed on the right side. Consequently, a 3-D video of microsurgery can be created by viewing the edited video by the cross-eyed stereogram viewing method without optical devices. The 3-D microsurgical video provides a more accurate view, especially with regard to depth, and a better understanding of microsurgical anatomy. Although several issues are yet to be addressed, this 3-D video system is a useful method of recording and presenting microsurgery for 3-D viewing with currently available equipment, without optical devices.

  7. Woodstock Scholarship : An Interdisciplinary Annotated Bibliography

    OpenAIRE

    Gatten, Jeffrey N.

    2016-01-01

    "Since August 1969, the Woodstock Music and Art Fair looms large when recounting the history and impact of the baby boom generation and the societal upheavals of the Sixties. Scholars study the sociological, political, musical, and artistic impact of the event and use it as a cultural touchstone when exploring alternative perspectives or seeking clarity. This interdisciplinary annotated bibliography records the details of over 400 English-language resources on the Festival, including books, c...

  8. Deburring: an annotated bibliography. Volume V

    Energy Technology Data Exchange (ETDEWEB)

    Gillespie, L.K.

    1978-01-01

    An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.

  9. Gastrointestinal hormone research - with a Scandinavian annotation

    DEFF Research Database (Denmark)

    Rehfeld, Jens F

    2015-01-01

    Gastrointestinal hormones are peptides released from neuroendocrine cells in the digestive tract. More than 30 hormone genes are currently known to be expressed in the gut, which makes it the largest hormone-producing organ in the body. Modern biology makes it feasible to conceive the hormones un......, but also constitute regulatory systems operating in the whole organism. This overview of gut hormone biology is supplemented with an annotation on some Scandinavian contributions to gastrointestinal hormone research....

  10. Deburring: an annotated bibliography. Volume VI

    Energy Technology Data Exchange (ETDEWEB)

    Gillespie, L.K.

    1980-07-01

    An annotated summary of 138 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese, and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a proces economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.

  11. Semantic Annotation of Video Fragments as Learning Objects: A Case Study with "YouTube" Videos and the Gene Ontology

    Science.gov (United States)

    Garcia-Barriocanal, Elena; Sicilia, Miguel-Angel; Sanchez-Alonso, Salvador; Lytras, Miltiadis

    2011-01-01

    Web 2.0 technologies can be considered a loosely defined set of Web application styles that foster a kind of media consumer more engaged, and usually active in creating and maintaining Internet contents. Thus, Web 2.0 applications have resulted in increased user participation and massive user-generated (or user-published) open multimedia content,…

  12. GLANET: genomic loci annotation and enrichment tool.

    Science.gov (United States)

    Otlu, Burçak; Firtina, Can; Keles, Sündüz; Tastan, Oznur

    2017-09-15

    Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET . Tutorials are provided at https://glanet.readthedocs.org . burcak@ceng.metu.edu.tr or oznur.tastan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online.

  13. Annotating breast cancer microarray samples using ontologies.

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-11-06

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology(MO). In this paper, we developed BCM-CO, anontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCMCO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations.

  14. Enzyme reaction annotation using cloud techniques.

    Science.gov (United States)

    Huang, Chuan-Ching; Lin, Chun-Yuan; Chang, Cheng-Wen; Tang, Chuan Yi

    2013-01-01

    An understanding of the activities of enzymes could help to elucidate the metabolic pathways of thousands of chemical reactions that are catalyzed by enzymes in living systems. Sophisticated applications such as drug design and metabolic reconstruction could be developed using accurate enzyme reaction annotation. Because accurate enzyme reaction annotation methods create potential for enhanced production capacity in these applications, they have received greater attention in the global market. We propose the enzyme reaction prediction (ERP) method as a novel tool to deduce enzyme reactions from domain architecture. We used several frequency relationships between architectures and reactions to enhance the annotation rates for single and multiple catalyzed reactions. The deluge of information which arose from high-throughput techniques in the postgenomic era has improved our understanding of biological data, although it presents obstacles in the data-processing stage. The high computational capacity provided by cloud computing has resulted in an exponential growth in the volume of incoming data. Cloud services also relieve the requirement for large-scale memory space required by this approach to analyze enzyme kinetic data. Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported.

  15. Enzyme Reaction Annotation Using Cloud Techniques

    Directory of Open Access Journals (Sweden)

    Chuan-Ching Huang

    2013-01-01

    Full Text Available An understanding of the activities of enzymes could help to elucidate the metabolic pathways of thousands of chemical reactions that are catalyzed by enzymes in living systems. Sophisticated applications such as drug design and metabolic reconstruction could be developed using accurate enzyme reaction annotation. Because accurate enzyme reaction annotation methods create potential for enhanced production capacity in these applications, they have received greater attention in the global market. We propose the enzyme reaction prediction (ERP method as a novel tool to deduce enzyme reactions from domain architecture. We used several frequency relationships between architectures and reactions to enhance the annotation rates for single and multiple catalyzed reactions. The deluge of information which arose from high-throughput techniques in the postgenomic era has improved our understanding of biological data, although it presents obstacles in the data-processing stage. The high computational capacity provided by cloud computing has resulted in an exponential growth in the volume of incoming data. Cloud services also relieve the requirement for large-scale memory space required by this approach to analyze enzyme kinetic data. Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported.

  16. Cadec: A corpus of adverse drug event annotations.

    Science.gov (United States)

    Karimi, Sarvnaz; Metke-Jimenez, Alejandro; Kemp, Madonna; Wang, Chen

    2015-06-01

    CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.(1). Copyright © 2015 Elsevier Inc. All rights reserved.

  17. dcGOR: an R package for analysing ontologies and protein domain annotations.

    Directory of Open Access Journals (Sweden)

    Hai Fang

    2014-10-01

    Full Text Available I introduce an open-source R package 'dcGOR' to provide the bioinformatics community with the ease to analyse ontologies and protein domain annotations, particularly those in the dcGO database. The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies including Gene Ontology. Although increasing in popularity, this database needs statistical and graphical support to meet its full potential. Moreover, there are no bioinformatics tools specifically designed for domain ontology analysis. As an add-on package built in the R software environment, dcGOR offers a basic infrastructure with great flexibility and functionality. It implements new data structure to represent domains, ontologies, annotations, and all analytical outputs as well. For each ontology, it provides various mining facilities, including: (i domain-based enrichment analysis and visualisation; (ii construction of a domain (semantic similarity network according to ontology annotations; and (iii significance analysis for estimating a contact (statistical significance network. To reduce runtime, most analyses support high-performance parallel computing. Taking as inputs a list of protein domains of interest, the package is able to easily carry out in-depth analyses in terms of functional, phenotypic and diseased relevance, and network-level understanding. More importantly, dcGOR is designed to allow users to import and analyse their own ontologies and annotations on domains (taken from SCOP, Pfam and InterPro and RNAs (from Rfam as well. The package is freely available at CRAN for easy installation, and also at GitHub for version control. The dedicated website with reproducible demos can be found at http://supfam.org/dcGOR.

  18. A new video programme

    CERN Multimedia

    CERN video productions

    2011-01-01

    "What's new @ CERN?", a new monthly video programme, will be broadcast on the Monday of every month on webcast.cern.ch. Aimed at the general public, the programme will cover the latest CERN news, with guests and explanatory features. Tune in on Monday 3 October at 4 pm (CET) to see the programme in English, and then at 4:20 pm (CET) for the French version.   var flash_video_player=get_video_player_path(); insert_player_for_external('Video/Public/Movies/2011/CERN-MOVIE-2011-129/CERN-MOVIE-2011-129-0753-kbps-640x360-25-fps-audio-64-kbps-44-kHz-stereo', 'mms://mediastream.cern.ch/MediaArchive/Video/Public/Movies/2011/CERN-MOVIE-2011-129/CERN-MOVIE-2011-129-Multirate-200-to-753-kbps-640x360-25-fps.wmv', 'false', 480, 360, 'https://mediastream.cern.ch/MediaArchive/Video/Public/Movies/2011/CERN-MOVIE-2011-129/CERN-MOVIE-2011-129-posterframe-640x360-at-10-percent.jpg', '1383406', true, 'Video/Public/Movies/2011/CERN-MOVIE-2011-129/CERN-MOVIE-2011-129-0600-kbps-maxH-360-25-fps-...

  19. Efficient Software HEVC to AVS2 Transcoding

    Directory of Open Access Journals (Sweden)

    Yucong Chen

    2016-09-01

    Full Text Available The second generation of Audio and Video coding Standard (AVS is developed by the IEEE 1857 Working Group under project 1857.4 and was standardized in 2016 by the AVS Working Group of China as the new broadcasting standard AVS2. High Efficient Video Coding (HEVC is the newest global video coding standard announced in 2013. More and more codings are migrating from H.264/AVC to HEVC because of its higher compression performance. In this paper, we propose an efficient HEVC to AVS2 transcoding algorithm, which applies a multi-stage decoding information utilization framework to maximize the usage of the decoding information in the transcoding process. The proposed algorithm achieves 11×–17× speed gains over the AVS2 reference software RD 14.0 with a modest BD-rate loss of 9.6%–16.6%.

  20. 78 FR 34370 - Revisions to Electric Quarterly Report Filing Process; Notice of Availability of Video Showing...

    Science.gov (United States)

    2013-06-07

    ... processes for filing EQRs allows an EQR seller and its agent to file using a web interface that generally replicates the Commission-distributed software used currently. A video showing how EQRs can be filed using...

  1. ViTexOCR; a script to extract text overlays from digital video

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The ViTexOCR script presents a new method for extracting navigation data from videos with text overlays using optical character recognition (OCR) software. Over the...

  2. Categorizing Video Game Audio

    DEFF Research Database (Denmark)

    Westerberg, Andreas Rytter; Schoenau-Fog, Henrik

    2015-01-01

    This paper dives into the subject of video game audio and how it can be categorized in order to deliver a message to a player in the most precise way. A new categorization, with a new take on the diegetic spaces, can be used a tool of inspiration for sound- and game-designers to rethink how...... they can use audio in video games. The conclusion of this study is that the current models' view of the diegetic spaces, used to categorize video game audio, is not t to categorize all sounds. This can however possibly be changed though a rethinking of how the player interprets audio....

  3. Brains on video games

    OpenAIRE

    Bavelier, Daphne; Green, C. Shawn; Han, Doug Hyun; Renshaw, Perry F.; Merzenich, Michael M.; Gentile, Douglas A.

    2011-01-01

    The popular press is replete with stories about the effects of video and computer games on the brain. Sensationalist headlines claiming that video games ‘damage the brain’ or ‘boost brain power’ do not do justice to the complexities and limitations of the studies involved, and create a confusing overall picture about the effects of gaming on the brain. Here, six experts in the field shed light on our current understanding of the positive and negative ways in which playing video games can affe...

  4. High Dynamic Range Video

    CERN Document Server

    Myszkowski, Karol

    2008-01-01

    This book presents a complete pipeline forHDR image and video processing fromacquisition, through compression and quality evaluation, to display. At the HDR image and video acquisition stage specialized HDR sensors or multi-exposure techniques suitable for traditional cameras are discussed. Then, we present a practical solution for pixel values calibration in terms of photometric or radiometric quantities, which are required in some technically oriented applications. Also, we cover the problem of efficient image and video compression and encoding either for storage or transmission purposes, in

  5. 3D video

    CERN Document Server

    Lucas, Laurent; Loscos, Céline

    2013-01-01

    While 3D vision has existed for many years, the use of 3D cameras and video-based modeling by the film industry has induced an explosion of interest for 3D acquisition technology, 3D content and 3D displays. As such, 3D video has become one of the new technology trends of this century.The chapters in this book cover a large spectrum of areas connected to 3D video, which are presented both theoretically and technologically, while taking into account both physiological and perceptual aspects. Stepping away from traditional 3D vision, the authors, all currently involved in these areas, provide th

  6. Open-source telemedicine platform for wireless medical video communication.

    Science.gov (United States)

    Panayides, A; Eleftheriou, I; Pantziaris, M

    2013-01-01

    An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN) and 3.5G high-speed packet access (HSPA) wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD) algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings.

  7. Open-Source Telemedicine Platform for Wireless Medical Video Communication

    Directory of Open Access Journals (Sweden)

    A. Panayides

    2013-01-01

    Full Text Available An m-health system for real-time wireless communication of medical video based on open-source software is presented. The objective is to deliver a low-cost telemedicine platform which will allow for reliable remote diagnosis m-health applications such as emergency incidents, mass population screening, and medical education purposes. The performance of the proposed system is demonstrated using five atherosclerotic plaque ultrasound videos. The videos are encoded at the clinically acquired resolution, in addition to lower, QCIF, and CIF resolutions, at different bitrates, and four different encoding structures. Commercially available wireless local area network (WLAN and 3.5G high-speed packet access (HSPA wireless channels are used to validate the developed platform. Objective video quality assessment is based on PSNR ratings, following calibration using the variable frame delay (VFD algorithm that removes temporal mismatch between original and received videos. Clinical evaluation is based on atherosclerotic plaque ultrasound video assessment protocol. Experimental results show that adequate diagnostic quality wireless medical video communications are realized using the designed telemedicine platform. HSPA cellular networks provide for ultrasound video transmission at the acquired resolution, while VFD algorithm utilization bridges objective and subjective ratings.

  8. Software attribute visualization for high integrity software

    Energy Technology Data Exchange (ETDEWEB)

    Pollock, G.M.

    1998-03-01

    This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

  9. Annotation Graphs: A Graph-Based Visualization for Meta-Analysis of Data Based on User-Authored Annotations.

    Science.gov (United States)

    Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam

    2017-01-01

    User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.

  10. Enhancing digital video analysis of bar kinematics in weightlifting: a case study

    OpenAIRE

    Dæhlin, Torstein Eriksen; Krosshaug, Tron; Chiu, Loren Z.F.

    2017-01-01

    Weightlifting technique can be objectively assessed from two-dimensional video recordings. Despite its importance, participants’ bar trajectories in research involving the snatch or clean exercises are often not reported, potentially due to the time required to digitize video. The purpose of this investigation was to evaluate the use of an LED-based marker, digital video and open source software to automatically track the bar end during weightlifting exercises. A former national-level weightl...

  11. Ontologies for software engineering and software technology

    CERN Document Server

    Calero, Coral; Piattini, Mario

    2006-01-01

    Covers two applications of ontologies in software engineering and software technology: sharing knowledge of the problem domain and using a common terminology among all stakeholders; and filtering the knowledge when defining models and metamodels. This book is of benefit to software engineering researchers in both academia and industry.

  12. Professional learning needs in using video calls identified through workshops.

    Science.gov (United States)

    Statton, Sarah; Jones, Ray; Thomas, Martin; North, Tracie; Endacott, Ruth; Frost, Adrian; Tighe, Dazzle; Wilson, Gail

    2016-05-10

    Most people want to die at home but only half do. Supporting patients in rural locations is challenging. Video calls such as Skype, might help but are not routinely used; we should consider learning needs to increase uptake and ensure effective use. We aimed to identify learning needs of healthcare professionals (HCPs) in using video calls to support patients (and their carers) to die at home. Face-to-face workshops were held in five Southwest England locations. Participants discussed advantages, disadvantages, scenarios for use, and the learning needs of video call users. Ideas were documented on flipcharts and discussions audio-recorded. The 116 participants included nurses, allied HCPs, doctors and previously bereaved volunteers. Lists of advantages, disadvantages, scenarios and learning needs were compiled and circulated to participants. In a subsequent online workshop, 21 participants ranked seven groups of learning needs in priority order. Most participants thought video calls could be used to advantage in many end-of-life scenarios, especially in rural areas. Seven themes, covering 59 learning needs for HCPs, were identified (in priority order): (i) confidence and technical ability in using video calls; (ii) being aware of how video calls fit into clinical practice; (iii) managing video calls; (iv) communication skills on 'camera'; (v) understanding how patients and families may be affected by video call use; (vi) presenting video calls as an option to patients and families to assess their readiness; (vii) normal professional skills that become essential for effective video calls. Although almost ubiquitous, video call software is not routinely and effectively used in British clinical practice. Supporting patients and families at end-of-life is one example where it could be used to advantage, but clinicians need to plan and practise before using it in real situations. Learning needs were identified that could be developed into learning modules and/or courses.

  13. ON USING VIDEO CONFERENCE SYSTEMS IN HIGHER SCHOOL FOR DISTANCE LEARNING

    Directory of Open Access Journals (Sweden)

    Д В Сенашенко

    2015-12-01

    Full Text Available The article describes distant learning systems used in world practice. The author gives classification of video communication systems. Aspects of using Skype software in Russian Federation are discussed. In conclusion the author provides the review of modern production video conference systems used as tools for distant learning.

  14. Using Video Streaming: Setting Up a Cheap System for Distributing Information to Teachers and Students

    Science.gov (United States)

    McNeal, Thomas, Jr.; Kearns, Landon

    2005-01-01

    Video streaming can be a very useful tool for educators. It is now possible for a school?s technical specialist or classroom teacher to create a streaming server with tools that are available in many classrooms. In this article we describe how we created our video streamer using free software, older computers, and borrowed hardware. The system…

  15. QoS control strategies for high-quality video processing

    NARCIS (Netherlands)

    Wüst, C.C.; Steffens, E.F.M.; Verhaegh, W.F.J.; Bril, R.J.; Hentschel, C.

    2005-01-01

    Video processing in software is often characterized by highly fluctuating, content-dependent processing times, and a limited tolerance for deadline misses. We present an approach that allows close-to-average-case resource allocation to a single video processing task, based on asynchronous, scalable

  16. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... Care Disease Types FAQ Handout for Patients and Families Is It Right for You How to Get ... For the Media For Clinicians For Policymakers For Family Caregivers Glossary Menu In this section Links Videos ...

  17. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... Donate Search Search What Is It Definition Pediatric Palliative Care Disease Types FAQ Handout for Patients and Families ... Policymakers For Family Caregivers Glossary Resources Browse our palliative care resources below: Links Videos Podcasts Webinars For the ...

  18. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... Click to learn more... LOGIN CALENDAR DONATE NEWS Home Learn Back Learn about acoustic neuroma AN Facts ... Vision & Values Leadership & Staff Annual Reports Shop ANA Home Learn Educational Video Ronson and Kerri Albany Support ...

  19. Videos, Podcasts and Livechats

    Medline Plus

    Full Text Available ... Donate Search Search What Is It Definition Pediatric Palliative Care Disease Types FAQ Handout for Patients and ... Policymakers For Family Caregivers Glossary Resources Browse our palliative care resources below: Links Videos Podcasts Webinars For ...

  20. Acoustic Neuroma Educational Video

    Medline Plus

    Full Text Available ... Click to learn more... LOGIN CALENDAR DONATE NEWS Home Learn Back Learn about acoustic neuroma AN Facts ... Vision & Values Leadership & Staff Annual Reports Shop ANA Home Learn Educational Video Howard of NJ Gloria hiking ...