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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.
Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.
Proper citation: GlyGen (RRID:SCR_023438) Copy
https://californiacoastalatlas.net/
Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes.
Proper citation: California Coastal Atlas (RRID:SCR_024554) Copy
http://mouse.brain-map.org/static/atlas
Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.
Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy
https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware
Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems.
Proper citation: Phantom Camera Control (RRID:SCR_021080) Copy
https://cran.r-project.org/package=wavethresh
Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Proper citation: wavethresh (RRID:SCR_024311) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.
Proper citation: PMAP (RRID:SCR_000740) Copy
https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation
THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.
Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/PICS.html
R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.
Proper citation: PICS (RRID:SCR_001093) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
http://www.type2diabetesgenetics.org/
Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.
Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
Proper citation: BioMart Project (RRID:SCR_002987) Copy
https://github.com/ABCD-STUDY/pearson-central-end-point
Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive.
Proper citation: pearson-central-end-point (RRID:SCR_016034) Copy
Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.
Proper citation: CMap (RRID:SCR_016204) Copy
https://github.com/mizutanilab/RecView
Software tool as a program for tomographic reconstruction and image processing of micro/nano-CT data taken at SPring8 and APS Argonne.
Proper citation: RecView (RRID:SCR_016531) Copy
http://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion
Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.
Proper citation: UMMPerfusion (RRID:SCR_015970) Copy
http://www.uimcimes.es/contenidos/golink?p=1
Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.
Proper citation: QModeling (RRID:SCR_016358) Copy
Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.
Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy
https://github.com/xsun28/CloudMerge/
Software for merging massive VCF files into a single VCF file or TPED file. Source codes can be slightly modified to fit into other types of sorted merging of Omics data.
Proper citation: CloudMerge (RRID:SCR_016051) Copy
http://www.jstacs.de/index.php/GeMoMa
Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.
Proper citation: GeMoMa (RRID:SCR_017646) Copy
https://github.com/BioDepot/BioDepot-workflow-builder
Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.
Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy
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