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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.

(last updated: Oct 5, 2019)

Physical Resource or Software Tool Software

16,556 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
3D surgical atlases of the murine headResource, atlas, data or information resource3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.129s1/svimj, anatomy, brain, c57bl/6j, central nervous system, digital atlas, imaging assay, in vivo, micro-electroporation, morphometric analysis, skull, sterotactic, transgenic, imagingSCR_008039(3D surgical atlases of the murine head, RRID:SCR_008039)University of Toronto; Ontario; Canada Canadian Institute for Health Research, NARSAD Young Investigator award, Ontario Research Development ChallengeLast checked upnif-0000-10249
MSClustResource, software resourceAn M software package for Clustering 16S rRNA sequences into operational taxonomic units (OTUs). The download link contain the package and some benchmark data sets.16s rrna, operational taxonomic unit, 16s rrna read, clustering algorithm, next-generation sequencing, seeds-selectionSCR_001773(MSClust, RRID:SCR_001773)Yale School of Medicine; Connecticut; USA listed by: OMICtoolsPMID:23899776Last checked upOMICS_01954
M-pickResource, software resourceA modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.16s rrna sequence, 16s rrna, rrna, sequence, binningSCR_004995(M-pick, RRID:SCR_004995)University of Florida; Florida; USA listed by: OMICtoolsLast checked upOMICS_01447
Database Enabled Code for Ideal Probe Hybridization Employing RResource, software resource, software toolkitA software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language.16s rrna sequence, chimera, primer, probe, array, 16s oligo, dna sequence, rSCR_000581(Database Enabled Code for Ideal Probe Hybridization Employing R, RRID:SCR_000581)University of Wisconsin-Madison; Wisconsin; USA listed by: OMICtoolsPMID:22101057Last checked upOMICS_01114
GramClusterResource, software resourceSoftware implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.16s sequence, clusterSCR_000272(GramCluster, RRID:SCR_000272)University of Nebraska; Nebraska; USA listed by: OMICtoolsPMID:21167044Last checked upOMICS_01956
Phelan-McDermid Syndrome FoundationResource, disease-related portal, topical portal, portal, community building portal, funding resource, data or information resourceThe Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.22q13 deletion syndrome, phelan-mcdermid syndrome, rare disease, genetic, meeting, child, chromosome 22, treatment, therapy, research, grant, fellowshipSCR_001707(Phelan-McDermid Syndrome Foundation, RRID:SCR_001707)Phelan-McDermid SyndromeLast checked upnif-0000-10203
Kendrick Labs - Proteomic Services Including 2D Gel Electrophoresis Western Blotting and Mass SpectrometryResource, organization portal, material analysis service, analysis service resource, production service resource, laboratory portal, service resource, portal, data or information resourceKendrick Labs has been carrying out protein electrophoresis as a service for academia, federal institutions and industry since 1987. It's mission is to help clients solve proteomic problems quickly and economically, especially problems which require 2-dimensional gel electrophoresis. The lab service functions nationwide via low-cost express mail, toll-free phone, and e-mail. It receive samples and return results to New York and Los Angeles as fast as labs based in these cities. It's goal is to help clients solve proteomic problems quickly and economically in a changing world. To that end it is now offering Phosphotyrosine Western Blotting with the PY20 monoclonal antibody and also Phosphoserine/Phosphothreonine Western Blotting with Qiagen antibodies.2-dimentional, antibody, monoclonal antibody, protein electrophoresis, protomic, qiagen, service, western blottingSCR_002914(Kendrick Labs - Proteomic Services Including 2D Gel Electrophoresis Western Blotting and Mass Spectrometry, RRID:SCR_002914)Last checked upnif-0000-30014
BrainNavigatorResource, atlas, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, imageSCR_008289(BrainNavigator, RRID:SCR_008289)Last checked downnif-0000-24037
Autodesk MeshmixerResource, data processing software, software application, data visualization software, 3d visualization software, software resource, authoring tool3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions.3d, 3d visualization, 3d printing, triangle mesh, 3d scan, 3d designSCR_015736(Autodesk Meshmixer, RRID:SCR_015736)submitted by: Resource Identification PortalPMID:28663663Last checked up
UCSF ChimeraXResource, data processing software, software application, data visualization software, 3d visualization software, 4d visualization software, software resourceSoftware for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.3d, 4d, image reconstruction, molecular visualization, biocomputing, informatics, rbvi, ucsf, chimeraSCR_015872(UCSF ChimeraX, RRID:SCR_015872)University of California at San Francisco; California; USA NIGMSrelated to: UCSF ChimeraLast checked down
V3DResource, segmentation software, image analysis software, data processing software, software application, data visualization software, software resource, d visualization softwareV3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, imageSCR_008646(V3D, RRID:SCR_008646)Janelia Research Howard Hughes Medical InstitutePMID:20231818Last checked upnif-0000-32975
Volocity 3D Image Analysis SoftwareResource, software resource, image analysis software, data processing software, commercial organization, software application3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience.3d, confocal microscopy, visualization, analyzeSCR_002668(Volocity 3D Image Analysis Software, RRID:SCR_002668)Last checked upSciRes_000112
Advanced 3D Visualization and Volume ModelingResource, data analysis software, data processing software, software application, data visualization software, 3d visualization software, software resourceSoftware tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.3d, data, visualization, tomography, imaging, process, MRI, microscopy, videoSCR_007353(Advanced 3D Visualization and Volume Modeling, RRID:SCR_007353)Last checked downnif-0000-00262, SCR_014305
MPIDBResource, data or information resource, databaseDatabase that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiologySCR_001898(MPIDB, RRID:SCR_001898)J. Craig Venter Institute Indgen Life Technologies, J. Craig Venter Institute, NIH, NIMHrelated to: IMEx - The International Molecular Exchange Consortium, IntAct, Database of Interacting Proteins, BIND, MINT, Interaction Reference Index, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, listed by: re3data.orgPMID:18556668Last checked downnif-0000-10467
3D GenomeResource, service resourceGenome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene.3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structureSCR_017525(3D Genome, RRID:SCR_017525)Pennsylvania State University related to: EncodeLast checked up
CIPRO: Ciona intestinalis Protein DatabaseResource, data or information resource, databaseCIPRO is an integrated protein database of the ascidian Ciona intestinalis. It has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advanced and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.3d imaging, ascidia, ciona intestinalis, intracellular localization, peptide mass fingerprintingSCR_007569(CIPRO: Ciona intestinalis Protein Database, RRID:SCR_007569)Last checked upnif-0000-02664
3DViewnixResource, software resource, software application, data processing software, d visualization softwareData-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code3d imaging, registration, segmentation, visualization, volume, multi-modal, imageSCR_007351(3DViewnix, RRID:SCR_007351)University of Pennsylvania; Philadelphia; Pennsylvania listed by: 3DVC, BiositemapsPMID:12821028Last checked upnif-0000-00257
Research Collaboratory for Structural Bioinformatics Protein Data BankResource, service resource, data or information resource, databaseCollection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standardSCR_012820(Research Collaboratory for Structural Bioinformatics Protein Data Bank, RRID:SCR_012820) Rutgers University; New Jersey; USA , University of California at San Diego; California; USA DOE, NIH, NSFrelated to: pdb-data, PDB2MultiGif, GlyProt, pdb-care, pdb2linucs, GlyVicinity, GlyTorsion, GlySeq, AffinDB, StatAlign, Community Structure-Activity Resource, Binding MOAD, ConSurf Database,, DOMINE: Database of Protein Interactions, Jenalib: Jena Library of Biological Macromolecules, SynSysNet, Unified Data Resource for Cryo Electron Microscopy, PDBe - Protein Data Bank in Europe, TFinDIT, HOLLOW, ccPDB - Compilation and Creation of datasets from PDB, DOMMINO - Database Of MacroMolecular INteractiOns, InterEvol database, Polbase, PoSSuM, ProtChemSI, RNA CoSSMos, PDBsum, Worldwide Protein Data Bank , canSAR, CAPS Database, Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING, Combinatorial Extension (CE), Metalloprotein Site Database, PDBj - Protein Data Bank Japan, Statistical Torsional Angles Potentials of NMR Refinement Database, Metalloprotein Ligand Interaction Database, CARP, PDBTM, RNA FRABASE - RNA FRAgments search engine and dataBASE, AmiGO, ConsensusPathDB, Biological Magnetic Resonance Data Bank, DDBJ - DNA Data Bank of Japan, FlyMine, NCBI Protein, NCBI Nucleotide, FunTree, IndelFR - Indel Flanking Region Database, NMR Restraints Grid, Enzyme Structures Database, Electron Microscopy Data Bank at PDBe, Worldwide Protein Data Bank , DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, MINAS - Metal Ions in Nucleic AcidS, RCSB PDB, PDBj - Protein Data Bank Japan, used by: SGC, Ligand Expo , DARC - Database for Aligned Ribosomal Complexes, FireDB, Protein Data Bank Bind Database, Protein Data Bank Site, NIF Data Federation, ChannelPedia, MobiDB, Protein Database, listed by:, affiliated with: Unified Data Resource for Cryo Electron Microscopy, ConSurf-DB, works_with: CellPhoneDBPMID:12037327Last checked upnif-0000-00135, SCR_017379,
Worldwide Protein Data Bank Resource, data or information resource, resource, databaseA free and public single global PDB archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standardSCR_006555( Worldwide Protein Data Bank , RRID:SCR_006555)BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, European Union, Japan Science and Technology Agency, NBDC - National Bioscience Database Center, NCI, NIDDK, NIGMS, NIH, NINDS, NLM, NSF, Wellcome Trustrelated to: Biological Magnetic Resonance Data Bank, Proteopedia - Life in 3D, NRG-CING, Research Collaboratory for Structural Bioinformatics Protein Data Bank, DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, PDBe - Protein Data Bank in Europe, PDBj - Protein Data Bank Japan, Biological Magnetic Resonance Data Bank, Research Collaboratory for Structural Bioinformatics Protein Data Bank, used by: Ligand ExpoPMID:14634627Last checked upnif-0000-23903
Allen Mouse Brain AtlasResource, atlas, service resource, database, data or information resource3D genome map of gene expression in adult mouse brain. Reveals expression patterns of genes throughout entire adult mouse brain down to cellular level. Interactive, genome wide image database of gene expression with ISH and Nissl images. Combination of RNA in situ hybridization data. Detailed Reference Atlases and informatics analysis tools are integrated to provide searchable digital atlas of gene expression.3D, map, gene, expression, data, adult, mouse, brain, interactive, imageSCR_002978(Allen Mouse Brain Atlas, RRID:SCR_002978)Allen Institute for Brain Science , Allen Brain Atlas related to: BrainStars, PubAnatomy, Integrated Brain Gene Expression, Allen Brain Atlas API, 3DBar, aGEM, CellTax vignette, used by: NIF Data Federation, works_with: MeshView, Brain Gene Expression Analysis toolboxLast checked upnif-0000-00508
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