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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/broadinstitute/pilon/
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
Proper citation: Pilon (RRID:SCR_014731) Copy
Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.
Proper citation: NeuroSynth (RRID:SCR_006798) Copy
https://github.com/StateSpaceModels
An open source library built to reduce technical friction and help modelers share their work. Models within SSM can be used for inference of time-series analysis.
Proper citation: State Space Models (RRID:SCR_014647) Copy
https://github.com/NeuroBox3D/AnaMorph
Framework for creating 3D neuronal morphologies from point/diameter descriptions.
Proper citation: AnaMorph (RRID:SCR_015012) Copy
A collection of big data analytics tools. FlashX performs data analytics in the form of graphs and matrices and utilize solid-state drives (SSDs) to scale to large datasets in a single machine. It has three main components: FlashGraph, FlashMatrix, and FlashR. FlashGraph is a general-purpose programming framework with a vertex-centric programming interface for large-scale graph analysis. FlashMatrix is a matrix computation engine that provides a small set of generalized matrix operations to express varieties of data mining and machine learning algorithms. FlashR is an extension of the R programming framework to process datasets at a scale of terabytes with the speed of optimized parallel C code.
Proper citation: FlashX (RRID:SCR_014536) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
