Curator Dashboard

JIV is a Java software for visualization and side-by-side comparison of multiple 3D image datasets. While it was originally designed for remote data access, it can be used as a traditional local application as well. It features include being highly portable and platform-independent, the ability to run with a common Web browser and to cope with slow network links, an independent 3D image data format, and a display of gray-level (intensity) image data with a user-controlled color-mapping, among other features.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.

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• SciCrunch
• 13 years ago - by Anonymous

Community group working towards a common, RDF-based, specification for annotating digital resources. The effort began by trying to reconcile two proposals: the Annotation Ontology (http://code.google.com/p/annotation-ontology/) and the Open Annotation Model (http://www.openannotation.org/spec/beta/ ). Initially, editors of these proposals collaborated to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. This draft became available for public feedback and experimentation in the second quarter of 2012. The final deliverable is a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback.

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• SciCrunch
• 13 years ago - by Anonymous

XV is an interactive image manipulation program for the X Window System. It can operate on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and if you have ghostscript (version 2.6 or above) installed on your machine, it can also display them. XV allows users to: display an image on the root window, in a variety of styles; grab any rectangular portion of the screen and turn it into an image; arbitrarily stretch, compress, rotate or flip the image; view files as ASCII text or hexadecimal data; determine pixel values and x,y coordinates in the image; apply different gamma functions to the Red, Green, and Blue color components, to correct for non-linear color response; and run a number of image-processing algorithms on any rectangular portion of the image, among other functions.

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• SciCrunch
• 17 years ago - by Anonymous

A program to merge paired end Illumina reads that are overlapping into a single longer read.

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• SciCrunch
• 13 years ago - by Anonymous

Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9,2023. Registry that archives curated nanomaterial research data and their biological and environmental implications. The Registry provides data management plans for researchers, and accepts users' public-ready data, archive them, integrate them into the registry, allowing for the data to be shared publicly. Users can request more information on specific nanomaterial records, compare multiple nanomaterials, and export data to their desktop.

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• SciCrunch
• 12 years ago - submitted by Yueling Li

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

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• SciCrunch
• 13 years ago - by Anonymous

A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).

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• SciCrunch
• 14 years ago - by Anonymous

A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work.

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• SciCrunch
• 15 years ago - by Anonymous

An institution and biomaterial supply resource which houses more than 3500 strains of algae. The majority of the strains are derived from freshwater/terrestrial habitats while 15% are representative of marine and brackish water strains. 15% of the strains are axenic. 50% of the strains are currently available to the public and can be ordered from the CCAC's main site.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code.

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• RRID
• 3 years ago - by Anonymous

Db for Dummies! is a small database that imports the Generic GO Slim. It allows data to be viewed in a tree. The Gene Ontology describes gene products in terms of their associated biological processes, cellular components and molecular functions. The Generic Slim Gene Ontology is a subset of the whole Gene Ontology. The slim version gives a broad overview and leaves out specific/fine grained terms. This example stores the slim version of the Gene Ontology (goslim_generic_obo) that can be downloaded from www.geneontology.org/GO.slims.shtml. Platform: Windows compatible

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• SciCrunch
• 15 years ago - by Anonymous

A web application which modifies the online use of scientific articles published in eLife. eLife Lens is a tool created by eLife that enables users to explore figures, figure descriptions, and references while keeping their place in the article text. Users can search for papers by subject, organism, article type, and/or top authors.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Flow cytometry studies optical parameters emitted by particles (cells, cell fractions). Flow cytometers can study a series of parameters of individual particles simultaneously, quickly and on a large number of individualized particles in suspension. Flow cytometers use lasers as a source of light excitement; therefore, it must be possible to mark the particles with one or more fluorescent substances. Information is also collected regarding the size and structural complexity of each particle. This multiparameter study of each particle enables us to analyse subpopulations in complex samples through electronic sorting. Some cytometers are also equipped with sorting and collection modules for particles of interest. The most important applications of flow cytometry include those relating to the study of cell surface receptors, nuclear and cytoplasmic antigens, DNA content, enzyme activity, cell integrity and membrane permeability and calcium flows. The Unit currently hosts five analyzers and two sorters, and is therewith the largest Becton Dickinson site in Spain. The sorters are operated by the facility personnel, who also support the users in experimental design and data analysis. The analyzers are operated by the users themselves, after they have been trained. The facility personnel helps with the experimental design and supervises and monitors the experiments when necessary.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A Parkinson's research foundation dedicated to finding a cure for Parkinson's disease and to ensuring the development of improved therapies. Pipeline Programs fund investigator-initiated proposals focused on the following critical points along the translational pathway to new therapies for Parkinson's disease.

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• SciCrunch
• 15 years ago - by Anonymous

An access service resource which serves as a global open access hub for the sharing and licensing of Biological Research Materials and related technologies with researchers. Biomedical researchers from research institutions and industry can connect with Technology Transfer Offices owning proprietary Biological Research Materials or rights to relevant technologies. Users can also search BioMedUSA's aggregated resources, such as biorepositotires and biologicals to share/license, for materials and technologies.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman