Curator Dashboard

An open source data sharing and visualization platform for neuroimaging data, that uses the OntoNeuroLOG ontology. Shanoir (Sharing NeurOImaging Resources) is an open source neuroinformatics platform designed to share, archive, search and visualize neuroimaging data. It provides a user-friendly secure web access and offers an intuitive workflow to facilitate the collecting and retrieving of neuroimaging data from multiple sources and a wizard to make the completion of metadata easy. Shanoir comes with many features such as anonymization of data, support for multicenter clinical studies on subjects or group of subjects. Shanoir offers an ontology-based data organization (OntoNeuroLOG). Among other things, this facilitates the reuse of data and metadata, the integration of processed data and provides traceability trough an evolutionary approach. Shanoir allows researchers, clinicians, PhD students and engineers to undertake quality research projects with an emphasis on remote collaboration. As a secured J2EE web application, it therefore allows you safely store and archive, with no more requirements than a computer with an internet connection. Furthermore, Shanoir is not only a web application: it is also a complete neuroinformatics platform in which you can easily integrate your existing processing tools or develop your own ones: see ShanoirTk. Shanoir is a project carried out by the VisAGeS Team, based at IRISA (INRIA Rennes - Bretagne Atlantique Research Centre). This software is released under QPL 1.0 license.

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• SciCrunch
• 14 years ago - by Anonymous

Access to semantically processed full-text of the open-access subset of PubMed Central. The RDF model and resulting dataset make extensive reuse of existing ontologies and semantic enrichment services. The entire enriched data set is available for download or via REST services. A SPARQL query interface to 10,000 enriched articles is available. The entire collection of RDF documents is available for download as a collection of ZIP files. Each document consists of three RDF files serialized as XML.

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• SciCrunch
• 14 years ago - by Anonymous

Portal to promote the activities of Swiss research groups working in the field of neuroinformatics, and encourage and facilitate collaborations both between them and with the wider International Neuroinformatics Coordinating Facility community. The initial focus is on neural reconstruction as a theme, both from image data acquired via light microscopy and electron microscopy; these data are invaluable for identifying neural circuits and the simulation and modelling of these systems. Open Source software packages developed for neuroinformatics in Switzerland and useful data sets provided by groups in Switzerland are freely available for use, subject to appropriate attribution.

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• SciCrunch
• 14 years ago - by Anonymous

Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.

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• SciCrunch
• 14 years ago - by Anonymous

A non-profit dedicated to ending neurofibromatosis (NF) through research. It is the leading nonprofit funding source of NF research in the world. The mission of The Children''s Tumor Foundation is to: * Encourage and support research and the development of treatments and cures for neurofibromatosis types 1 and 2, schwannomatosis, and related disorders (hereafter collectively referred to as NF); * Support persons with NF, their families, and caregivers by providing thorough, accurate, current, and readily accessible information; * Assist in the development of clinical centers, best practices, and other patient support mechanisms (but not including direct medical care) to create better access to quality healthcare for affected individuals; and, * Expand public awareness of NF to promote earlier and accurate diagnoses by the medical community, increase the non-affected population''s understanding of the challenges facing people with NF, and encourage financial and other forms of support from public and private sources. Through the implementation of the Foundation''s research initiatives, progress is being made on all fronts and for all types of NF; from discovery studies understanding the molecular signaling deficits that cause the manifestations of NF to the growth of preclinical drug screening initiatives and the emergence of a growing number of clinical trials. The Foundation advances research through strategically integrated programs that speed therapies from the lab to the patient.

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• SciCrunch
• 14 years ago - by Anonymous

A trusted third-party gatekeeper of patient data from participants in a rare disease ecosystem, collecting and managing the information in a scalable, cost-effective manner. Each patient registry provides critical disease knowledge which makes that disease easier to study, increasing the probability a treatment can be developed. PatientCrossroads takes a network approach to patient registry programs. Unlike companies that merely sell registry software, we offer a full range of administration, management, and genetic curation services. What does this consolidated, patient-centric approach to patient registries mean? * Patients can more easily find registries and provide their valuable data (including locations of blood and tissue samples as well as reports of diagnoses, disease symptoms, treatment usage, and lifestyle activities) * Patients can be confident in the privacy of their de-identified data and the knowledge that PatientCrossroads does not sell patient data * Researchers and pharmaceutical companies have a larger, more easily accessible pool of potential patients for research studies and clinical trials targeting specific rare diseases * Pharmaceutical companies can collect post-market surveillance data in a more scalable and cost-effective manner * Rare disease advocacy and research foundations can more easily organize their global patient populations for inclusion in trials and studies

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• SciCrunch
• 14 years ago - by Anonymous

A toolkit designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation. Features: * Fast terabyte-scale image data browsing * Collaborative microcircuit reconstruction and annotation * Flexible hierarchical semantic annotation * Multiple linked image stack display * Neuron Catalog * SVG and WebGL-based neuronal morphology viewer * Open source software

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• SciCrunch
• 14 years ago - by Anonymous

A patient registry to identify people with neurofibromatosis (NF) who are interested in participating in clinical trials, as well as determining the commonality of specific characteristics of NF. The NF Registry is committed to secure methodologies and pioneering research that will lead to improving the health and well-being of individuals and families affected by NF. This registry has been created to collect data on large numbers of people with NF. This has never existed before and will help: * Identify people who may be eligible for clinical trials or other research studies being conducted in the field of NF. New clinical trials are launched each year yet challenges identifying participants too often mean that these studies finish late or never really get started. Today, 80 percent of trials fail to recruit enough volunteers within planned timelines. Under enrollment is one of the most significant problems facing NF drug development. Together, we can solve it. * Determine the commonality of specific NF characteristics. This will help researchers and doctors devise better ways to care for people with NF If you or your child has been diagnosed with neurofibromatosis (NF) please join the NF Registry today. It''s quick, it''s easy, and it matters. The key to treatments lies within you researchers can''t deliver treatments without committed volunteers.

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• SciCrunch
• 14 years ago - by Anonymous

Collegiate university based in Dunedin, Otago, New Zealand.

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• SciCrunch
• 17 years ago - submitted by Stephen Larson

University in Norway, located in Oslo. Its faculties include Lutheran Theology, Law, Medicine, Humanities, Mathematics, natural sciences, social sciences, Dentistry, and Education.

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• SciCrunch
• 17 years ago - submitted by Eddy Kim

A database of elecrophysiological properties text-mined from the biomedical literature as a function of neuron type. Specifically, NeuroElectro seeks to extract information about the electrophysiological properties (e.g. resting membrane potentials and membrane time constants) of diverse neuron types from the existing literature and place it into a centralized database. There are 252 neurons currently available, with the naming convention established in NeuroLex.

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• SciCrunch
• 14 years ago - by Anonymous

An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community

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• SciCrunch
• 14 years ago - by Anonymous

A prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. It consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation. There are five key components involved in making HyBrow work. # The Event-based ontology for representing biological knowledge # The Discreet Event Systems based conceptual framework which provides the theory that allows us to make statements in a context free formal language (made up of the ontology) and evaluate the statements for validity using constraints declared on existing data # The rule library that provides the steps to apply those constraints and decide support, contradiction or no comment. # The relational database that stores existing information structured into the ontology. # The user interface.

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• SciCrunch
• 16 years ago - by Anonymous

A biomedical ontology in the vaccine domain

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 13, 2012. Cell Press continues to evolve the way scientific information is conveyed, and has made Article of the Future available for all review article formats, in addition to the research article format launched in January. With this latest release, all articles are also now more customizable, giving users added flexibility and control over how they read research and reviews. Readers can now: * Adjust the widths of the text and figure panels using a horizontal slider, allowing text and figures to be viewed side-by-side in a way that best suits the readers' needs. (Available in the Summary and Main Text tabs for reviews, and in the Results tab for research articles) * Easily identify proteins and small molecules and access additional information about these compounds with Reflect, winner of the 2009 Elsevier Grand Challenge * Reveal greater detail in figures with improved zoom functionality * Search across all tabs within an article * View the article in the standard, linear format with one click

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• SciCrunch
• 14 years ago - by Anonymous

Public flagship research university in Eugene, Oregon, United States.

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• SciCrunch
• 16 years ago - submitted by Stephen Larson

The NeuroSys Data Management System is a set of software tools created to enhance the process of data annotation, analysis and web publication. The system provides a set of easy to use software tools for data sharing by the scientific community. It enables researchers to build their own custom designed data management systems. Another branch of the system provides tools for viewing anatomical and physiological data. The initial implementation of the software, simply called NeuroSys, allowed users to create XML databases. Centered on a Java-based client application, it provided a way to design and construct custom GUI screens for data entry, data query and retrieval. It also automatically created a controlled vocabulary and supported the extension and/or migration of that vocabulary to whatever standard might be chosen at a later date. Most importantly, it empowered end-users to carry out all of these operations without the expertise and expense of trained database programmers. Right now a transition is underway, converting NeuroSys into a web-based application called Yogo. Yogo will retain all of functionality of NeuroSys, while adding new features. The new features will include automated data import from laboratory devices (such as microscopes and amplifiers), and a limited scope HTML editor to make data collections available on the web. Another component of the system is MIEN, a suite of data visualization and analysis tools. MIEN is intended for viewing anatomical and physiological data, and for annotating neuronal models.

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• SciCrunch
• 17 years ago - by Anonymous

ROM is an on-line Registry of Outcome Measures and associated tools designed to give guidance, information and assistance to international collaborative teams of reviewers undertaking the crucial task of choosing the right outcome measures (OMs) for neuromuscular disease trials and studies. It is also hoped that the Registry will reduce duplication of effort in this area. Outcome measures are the tests that investigators perform to decide whether a treatment being tested in a clinical trial is having any effect. These can come in many different forms from assessing how far a patient can walk in six minutes to looking at changes in their muscle through a biopsy and using the right outcome measure is a vital step in making sure a trial can really prove whether or not a treatment works. The searchable Registry contains information about OMs, such as a description, details of validation, availability, contact details for providers, and references to related documents including manuals and training videos. Review teams can record OMs by category as being considered for a specific study or trial and benefit from seeing the OM choices being considered by other review teams. A manual gives advice on how to assess and select OMs. Information contained in ROM may also prove useful to doctors, clinicians, physiotherapists, industry and other organizations with an interest in OMs relevant to NMD research.

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• SciCrunch
• 16 years ago - by Anonymous