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PubMed2026

BRIDGE: an interactive application for multi-omics data analysis, visualization and integration.

SUMMARY: BRIDGE is a Shiny-based application that provides an accessible, modular platform for individual and integrative multi-omics analysis. Using an independent SQLite database backend, it offers a local, private, and user-friendly environment that requires no prior computational expertise. The application supports proteomics, phospho-proteomics, and RNA-seq analyses through a comprehensive suite of visualization and analytical modules, together with an integrated multi-omics analysis pipeline. Built-in caching and asynchronous processing improve responsiveness, enabling efficient exploration, analysis, and visualization of multi-omics datasets on moderate hardware. AVAILABILITY AND IMPLEMENTATION: BRIDGE is implemented in R using Shiny and is freely available as a Docker container at https://ghcr.io/paulilab/bridge. A public demonstration server with example datasets is available at https://bridge.imp.ac.at. Code and datasets are also available at https://github.com/paulilab/BRIDGE and under DOI: https://doi.org/10.5281/zenodo.20215824.

Multiomics↗
PubMed2004

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets.

Animals↗
PubMed2019

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

Child↗
PubMed1992

Some tools for the diffusion of biomedical information using research networks.

Research and academic computer networks provide e-mail and other services to all members of participating institutions. Their usage by biomedical researchers and clinicians is still limited because of several reasons, including limited awareness of the available network resources. An increased use of these networks within the biomedical community would allow fast, effective communications and convenient remote access to information sources. As an example and pilot study, we prepared two network tools to make some information services maintained by our institution also accessible through e-mail. Both tools were implemented using PMDF e-mail software on a DEC MicroVAX connected to the Italian academic and research network (GARR), which is linked to the U.S. Internet. A network server takes care of automatic distribution of documents (files) reporting results of an oncology research/education project. An information server provides for semiautomated support of a consulting service on use of drugs. The feasibility of implementing these tools, based on existing software, further illustrates the potential usefulness of research computer networks for the dissemination of biomedical information.

Computer Communication Networks↗
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↗