The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of ...Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
The immune epitope database (IEDB) 3.0 Vita, Randi; Overton, James A; Greenbaum, Jason A ...
Nucleic acids research,
01/2015, Letnik:
43, Številka:
Database issue
Journal Article
Recenzirano
Odprti dostop
The IEDB, www.iedb.org, contains information on immune epitopes--the molecular targets of adaptive immune responses--curated from the published literature and submitted by National Institutes of ...Health funded epitope discovery efforts. From 2004 to 2012 the IEDB curation of journal articles published since 1960 has caught up to the present day, with >95% of relevant published literature manually curated amounting to more than 15,000 journal articles and more than 704,000 experiments to date. The revised curation target since 2012 has been to make recent research findings quickly available in the IEDB and thereby ensure that it continues to be an up-to-date resource. Having gathered a comprehensive dataset in the IEDB, a complete redesign of the query and reporting interface has been performed in the IEDB 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. We here present this most recent release of the IEDB and describe the user testing procedures as well as the use of external ontologies that have enabled it.
A challenge in presenting augmenting information in outdoor augmented reality (AR) settings lies in the broad range of uncontrollable environmental conditions that may be present, specifically ...large-scale fluctuations in natural lighting and wide variations in likely backgrounds or objects in the scene. In this paper, we present a active AR testbed that samples the user's field of view, and collects outdoor illuminance values at the participant's position. The main contribution presented herein is a user-based study (conducted using the testbed) that examined the effects on user performance of four outdoor background textures, four text colors, three text drawing styles, and two text drawing style algorithms for a text identification task using an optical, see-through AR system. We report significant effects for all these variables, and discuss design guidelines and ideas for future work
RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific ...expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.
RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data.
RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal.
anwarren@vt.edu
Supplementary materials are available at Bioinformatics online.
The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of ...Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types e.g. genomics, transcriptomics, protein– protein interactions (PPIs), three-dimensional protein structures and sequence typing data and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.
Interactive system developers are increasingly including usability engineering as an integral part of interactive system development. With recognition of the importance of usability come attempts to ...structure this new aspect of overall system development, leading to a variety of processes and methodologies. Unfortunately, these processes often lack flexibility, customizability, completeness, and breadth of coverage. This paper describes our development of a meta process or
process model that we call the Wheel. This innovative approach to creating and tailoring usability engineering processes addresses these shortcomings, and describes an evaluation of its application in a real-world commercial development environment.
The Wheel process model for usability engineering is
not a process itself, but instead, it provides a general framework into which developers can fit specific existing or new techniques, methods, or activities to apply “best usability practices”. It grew out of our examination, adaptation, and extension of several existing usability engineering and software methodologies. The methods that most strongly guided creation of the Wheel were the LUCID framework of interaction design, the Star life cycle of usability engineering, and the waterfall and spiral models of software engineering. The resulting process model assumes the form of a sequence of distinct cycles (each of which produces a product form), allowing developers to focus on each cycle separately. Each cycle has the same four activity types: Analyze, Design, Implement, and Evaluate. Each activity type in a cycle is instantiated using an existing usability engineering technique.
Working with an Internet technology company in northern Virginia under grant sponsorship from the Virginia Center for Innovative Technology (a research and development incubator for the Commonwealth of Virginia), we instantiated the Wheel process model and used it to develop a Web-based device management system. The process model performed remarkably well for this development environment, overcoming the tight constraints of budget and schedule cuts to produce an excellent process instance that resulted in a demonstration prototype of the company’s target system.
A fundamental problem in optical, see-through augmented reality (AR) is characterizing how it affects the perception of spatial layout and depth. This problem is important because AR system ...developers need to both place graphics in arbitrary spatial relationships with real-world objects, and to know that users will perceive them in the same relationships. Furthermore, AR makes possible enhanced perceptual techniques that have no real-world equivalent, such as x-ray vision, where AR users are supposed to perceive graphics as being located behind opaque surfaces. This paper reviews and discusses techniques for measuring egocentric depth judgments in both virtual and augmented environments. It then describes a perceptual matching task and experimental design for measuring egocentric AR depth judgments at medium- and far-field distances of 5 to 45 meters. The experiment studied the effect of field of view, the x-ray vision condition, multiple distances, and practice on the task. The paper relates some of the findings to the well-known problem of depth underestimation in virtual environments, and further reports evidence for a switch in bias, from underestimating to overestimating the distance of AR-presented graphics, at 23 meters. It also gives a quantification of how much more difficult the x-ray vision condition makes the task, and then concludes with ideas for improving the experimental methodology.
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