Curator Dashboard

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

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 05, 2013. It has been superseeded by the CALATK, available here http://www.calatk.org c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are: * LDDM: Fluid registration between two images. * TimeSeries: Time series analysis of longitudinal data for a single subject. * AtlasBuilder: Cross-sectional atlas building for a population of images. * LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set. * FRATUtils: A collection of utility functions for working with volumes and time series files

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• SciCrunch
• 14 years ago - by Anonymous

An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.

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• SciCrunch
• 6 years ago - by Anonymous

Ontology that provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.

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• SciCrunch
• 13 years ago - by Anonymous

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

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• SciCrunch
• 8 years ago - submitted by Jie Yang

Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.

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• SciCrunch
• 16 years ago - by Anonymous

A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task.

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• RRID
• 3 years ago - submitted by Samantha White