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At least 73 records · Page 4Linked to original sources
PubMed2002

Apollo: a sequence annotation editor.

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects.

Animals↗
PubMed2005

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

Computational Biology↗
PubMed2024

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.

User-Computer Interface↗
PubMed1992

EEG classification by learning vector quantization.

EEG classification using Learning Vector Quantization (LVQ) is introduced on the basis of a Brain-Computer Interface (BCI) built in Graz, where a subject controlled a cursor in one dimension on a monitor using potentials recorded from the intact scalp. The method of classification with LVQ is described in detail along with first results on a subject who participated in four on-line cursor control sessions. Using this data, extensive off-line experiments were performed to show the influence of the various parameters of the classifier and the extracted features of the EEG on the classification results.

Algorithms↗
PubMedDate not supplied

An intra-oral access device.

Using developments from the science of electropalatography, an intra-oral access device is being developed which increases the range and sensitivity of control available to the severely physically disabled individual. The system provides the user with a consistent positional relationship between the tongue and sensor in contrast to extra-oral mounted tongue switches. The system allows the tongue to function within the oral cavity where it has maximum speed, agility and mobility and gives the user a chance to increase accuracy through practice. A major benefit of this system is its versatility. By covering the surface area of the plate with a large number of sensors, the groups of sensors that are programmed to act as switches can take any size, shape, position and number to match the user's needs and abilities. As with any developing system, a number of problems have been encountered in practical use.

Adolescent↗
PubMedDate not supplied

A picture communicator for symbol users and/or speech-impaired people.

There are several approaches to producing communication aids for people with disabilities. The system described here takes the approach of utilizing as much mainstream hardware as possible, and adapting it with some modular software tools which have been designed to facilitate the building of customized symbol communication systems. The target audience are clients who are symbol users and/or have a speech impairment. The system provides several levels of screens, each of which can contain grids of scalable icons. A number of input methods are provided including keyboard, switch, mouse and touch-screen. Digitized and/or text to speech synthesis can be used for reinforcement of selections and for communication. The structure of the system is discussed and initial feedback from the first field trials is presented.

Communication Devices for People with Disabilities↗
PubMedDate not supplied

An entity-relation model for a tocho-gynaecology service.

There is a trend, both at national and European levels, towards the use of standards in hardware, software and communications. This implies a common root for the design of unified databases which will result in the homogeneity and interchangeability of data and knowledge. The technological solution exists and is imposed. The problem then is not the tools to be used as information support but how this information is organized and structured. According the the standards proposed by the Plan de Dotación Informática para la Asistencia Sanitaria (DIAS), and with respect to the problem of computer coverage of specialties, we present in this work an entity-relation model for a generic service within our project of integrally computerizing a tocho-gynaecology area. It is a multidisciplinary job between doctors and physicists where we use a planning strategy in order to identify the functions, processes and activities, making the traditional clinical management structure compatible with the one proposed. This means that if we want the introduction of the system to be effective, we have to make all the clinical and sanitary staff participate in the project. We must induce the need for change and carry out the process of change gradually, so that only a change in the support, and not in the organization, is initially perceived.

Algorithms↗
PubMedDate not supplied

Feasibility of interactive videodisc technology to teach minority youth about preventing HIV infection.

Hispanic and African American adolescents are more likely than white Anglo youth to harbor misconceptions about acquired immunodeficiency syndrome (AIDS) and are also more likely to engage in intravenous drug use and sexual intercourse. This paper describes the development of an AIDS prevention curriculum that uses an interactive videodisc program to teach skills for interventions. Focus group and expert panel studies yielded suggests for intervention vignettes and scenes relevant to Hispanic and African American adolescents. The authors then developed and produced a sample curriculum, specifically designed for Hispanic youth. Content was designed to build knowledge, attitudes, and skills in handling situations where young persons are at risk for human immunodeficiency virus (HIV) infection. The feasibility of the finished pilot product was tested with adolescents and with professionals who serve ethnic and racial minority youth. Adults and Hispanic adolescent viewers rated the videodisc as enjoyable, interesting, and likely to achieve positive effects with the intended target population. Findings suggest that the interactive videodisc is a useful way to interest and help Hispanic adolescents learn ways of reducing their risk of contracting and spreading HIV infection through lifestyle practices. This developmental research in the use of interactive videodisc also provides a basis for further investigation.

Adolescent↗