Curator Dashboard

A virtual database currently indexing multiple podcast resources including: The Brain Science Podcast, Nature Podcast, NeuroPod, Science Podcast, The American Journal of Psychiatry Podcast, 60-Second Mind, and Science Talk.

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• SciCrunch
• 14 years ago - by Anonymous

A web application which stores and organizes scholarly papers and references. Papers of interest identified from the web can be added to the users' personal library and the associated references will be automatically extracted.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Provides histological services as well as technical support. Equipped with ventilated working areas and equipment to prepare, process and stain frozen or paraffin embedded specimens. Instrumentation include VIP Tissue Processor, BIOCARE NxGen Decloaking Chamber, Rotary Microtome, Staining Center, Leica Cryostat, Zeiss Axio Microscope/Camera Software, Leica Bond-Max Immunostainer, Leica Autostainer XL, General Data Laser Cassette Marker.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information.

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• SciCrunch
• 15 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 Kristen Jensen

Extension to PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Preferred reporting items for systematic reviews and meta analyses literature search extension. Complements PRISMA Statement and its extensions by providing checklist that could be used by interdisciplinary authors, editors, and peer reviewers to verify that each component of search is completely reported and therefore reproducible.

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• RRID
• 3 years ago - by Anonymous

ZiFDB is a database of zinc finger arrays and zinc finger proteins organized for use by molecular biologists. ZiFDB organizes information on both individual zinc finger modules and engineered ZFAs. There are currently four sets of zinc finger modules available: 1) Sangamo BioScience researchers have identified fingers recognizing all 5''-GNN-3'' and a few of 5''-ANN-3'', 5''-CNN-3'' and 5''-TNN-3'' triplets using phage display, targeted mutagenesis and SELECT methods (Liu et al., 2002); 2) the Barbas group constructed another set of models, which recognize all 5''-GNN-3'', most 5''-ANN-3'', 5''-CNN-3'' and a few 5''-TNN-3'' triplets (Dreier et al., 2001; Dreier et al., 2005; Dreier et al., 2000;); 3) Toolgen, Inc. isolated a set of naturally-occurring zinc finger modules from human transcription factors (Bae et al., 2003); 4) the Joung lab has made a large number of ZFAs by OPEN, and the constituent zinc fingers are included in the database. For the engineered ZFAs, we have collected information on 3-finger ZFAs, since this is the architecture advocated by the Zinc Finger Consortium (http://www.zincfingers.org), a group of academic laboratories dedicated to the development of improved methods to engineer zinc finger proteins. Currently, all ZFAs in ZiFDB are described in the published literature. In the future, unpublished ZFAs will also be included. It is hoped that the information in this database will help molecular biologists develop zinc finger reagents that meet their needs for genome modification. Further, we hope the analysis of the collected information will aid in improving modular design.

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• SciCrunch
• 17 years ago - by Anonymous

A gene-based score intended to help in the interpretation of human sequence data. The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has. A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as intolerant.

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• SciCrunch
• 12 years ago - submitted by Slavé Petrovski

Software R package provides quality control and semantic enrichment tools for preparation of health datasets. Enables semantic enrichment of dataset where metavariables are discovered from relationships between input variables determined from user provided ontologies.

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• RRID
• 3 years ago - submitted by Tom Toner

CurePSP+ is an organization dedicated to increasing awareness of progressive supranuclear palsy, corticobasal degeneration, and related disorders, advancing research toward a cure, educating health professionals, and providing support, education and hope for persons with PSP, CBD and their families. PSP provides a number of resources, including a research grants/funding program, support for patients and families, educational materials, and PSP-related events. Patient and family support services include an online magazine, a resources guide, an educational center that provides The Guide for Persons with PSP, videos, support group meetings, and outreach and education brochures and conferences. In addition, CurePSP offers ART2CURE, a program of CurePSP (The Society for Progressive Supranuclear Palsy) that helps to generate essential revenue for research, advocacy, outreach, education and operating through the promotion and sale of artwork provided by various artists throughout the country. CurePSP is located in Hunt Valley, Maryland. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.

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• SciCrunch
• 17 years ago - by Anonymous

A software application which assists scientists with designing computational experiments. WINGS is a semantic workflow system which incorporates semantic constraints about datasets and workflow components into its workflow representations. The workflow system has an open modular design and can be easily integrated with other existing workflow systems and execution frameworks to extend them with semantic reasoning capabilities. WINGS also allows users to express high-level descriptions of their analysis goals, and assists them by automatically and systematically generating possible workflows that are consistent with that request. In cases where privacy or off-line use are important, WINGS can submit workflows in a scripted format for execution in the local host. It uses Pegasus or OODT as the execution engine for large-scale distributed workflow execution.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Web tool to analyze survival data by single year of diagnosis and estimates changes in survival trends and year over year trend measures.

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• RRID
• 3 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool that compares two gene expression signatures. Each signature is processed as a ranked list based on expression differences between two classes of samples. The signatures can be input either as raw expression data and sample and class labels, or as a preranked gene list.

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• SciCrunch
• 12 years ago - submitted by James Go

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.

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• SciCrunch
• 13 years ago - by Anonymous

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

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• SciCrunch
• 12 years ago - by Anonymous

Voluntary, non-profit organization dedicated to collecting and disseminating statistical data. Resource for gathering and disseminating epidemiologic data on all primary benign and malignant brain and other CNS tumors.

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• SciCrunch
• 16 years ago - by Anonymous

A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen