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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 12, 2019)

Physical Resource or Software Tool Software

16,890 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ProteinLynx Global ServerResource, organization portal, service resource, portal, data or information resourcePlatform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.Waters Corporation, quantitative, qualitative, proteomics, research, systemSCR_016664(ProteinLynx Global Server, RRID:SCR_016664)Last checked upwww.waters.com
InVesalius 3Resource, software resource, image reconstruction software, software application, data processing software, image analysis softwareSoftware for magnetic resonance image reconstruction and computed tomography reconstruction. Its main application geared towards rapid prototyping, teaching, forensics, and medicine. Its features include the ability to import DICOM or Analyze files, to export files to the STL, OBJ, and PLY formats, volume rendering, and manual or semiautomatic image segmentation.magnetic resonance image, magnetic resonance, image reconstruction, computed tomography reconstruction, computed tomography, image reconstruction softwareSCR_014693(InVesalius 3, RRID:SCR_014693)submitted by: Resource Identification PortalLast checked upwww.softwarepublico.gov.br
PhenoGOResource, data or information resource, databasePhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA).SCR_013646(PhenoGO, RRID:SCR_013646)University of Arizona; Arizona; USA related to: WormBase, SGD, Gene Ontology, Mouse Genome Informatics (MGI), FlyBase, uses: WormBase, SGD, Gene Ontology, Mouse Genome Informatics (MGI), FlyBaseLast checked upnlx_152722www.phenogo.org
HKL-2000Resource, , data processing software, software application, 3-d visualization software, software resource, software toolkit, simulation softwareSoftware package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.structural biology, structure determination process, simulation, 3d processing, mosaicity, strategySCR_015547(HKL-2000, RRID:SCR_015547)submitted by: Resource Identification PortalPMID:27754618Last checked upwww.hkl-xray.com
German Neuroinformatics NodeResource, topical portal, portal, data or information resourcePortal used to coordinate activities of the German portion of the INCF group. The main focus is the development and free distribution of software tools for handling and analyzing neurophysiological data.database, literature, metadata, neuroinformatics, ontology, portal, softwareSCR_007279(German Neuroinformatics Node, RRID:SCR_007279)Ludwig-Maximilians-University; Bavaria; Germany German Federal Ministry of Education and ResearchLast checked upnif-0000-00034www.g-node.org
Object-ImageResource, software resource, image analysis software, data processing software, software applicationImage analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter.image marking, non-destructive, image analysis, text editor, debugging softwareSCR_015720(Object-Image, RRID:SCR_015720)related to: NIH Image, submitted by: Resource Identification PortalLast checked downsimon.bio.uva.nl/Object-Image/object-image.html
SEDPHATResource, software resource, software application, data analysis software, data processing softwareSoftware for the global analysis of sedimentation velocity, sedimentation equilibrium, and/or dynamic light scattering experiments. It is a stand-alone sedimentation equilibrium analysis software that also processes isotherms of weight-average sedimentation coefficients, weight-average molar mass values, and other components.sedimentation, isotherm, velocity, molar, mass, isothermal, titration, calorimetry, sedfitSCR_016254(SEDPHAT, RRID:SCR_016254)PMID:17192587Last checked upsedfitsedphat.nibib.nih.gov
Mutation SurveyorResource, software resource, software application, sequence analysis software, data analysis software, data processing softwareSoftware for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.dna, sequencing, dna-seq, sanger sequencing, sequence analysis softwareSCR_001247(Mutation Surveyor, RRID:SCR_001247)listed by: OMICtoolsLast checked downOMICS_01816Mutation Surveyor software version 5.0http://www.softgenetics.com/mutationSurveyor.html
Zebrafish Information NetworkResource, service resource, data or information resource, data repository, storage service resource, databaseModel organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standardSCR_002560(Zebrafish Information Network, RRID:SCR_002560)University of Oregon; Oregon; USA NHGRIrelated to: AmiGO, Phenoscape Knowledgebase, MONARCH Disease Models View, Bgee: a dataBase for Gene Expression Evolution, NIH Data Sharing Repositories, HomoloGene, Zebrafish International Resource Center, Integrated Manually Extracted Annotation, Zebrafish Genome Project, used by: NIF Data Federation, Monarch Initiative, Resource Identification Portal, Morpholino Database, Integrated Animals, uses: InterMOD, recommended by: Resource Identification Portal, listed by: OMICtools, InterMOD, re3data.orgReferences (3)Last checked upnif-0000-21427, OMICS_01666, SCR_017504http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions
Zebrafish Brain AtlasResource, reference atlas, service resource, storage service resource, atlas, image repository, data repository, data or information resourceCollates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repositorySCR_000606(Zebrafish Brain Atlas, RRID:SCR_000606)University College London; London; United Kingdom BBSRC, European Union, Wellcome Trustrecommends: Zebrafish Anatomical Ontology, listed by: One Mind Biospecimen Bank ListingLast checked upnlx_149455http://zebrafishucl.org/
Zebrafish International Resource CenterResource, antibody supplier, material analysis service, analysis service resource, biomaterial supply resource, production service resource, service resource, storage service resource, biomaterial analysis service, reagent supplier, material storage repository, material resource, organism supplierCenter that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.zebrafish line, expressed sequence tag, cdna, fish, antibody, pathology, research, embryo, adultSCR_005065(Zebrafish International Resource Center, RRID:SCR_005065)University of Oregon; Oregon; USA NCRR, NICHD, NIH Office of the Director, W.M. Keck Foundationrelated to: One Mind Biospecimen Bank Listing, ZMP, NIF Data Federation, Zebrafish Information Network, zfishbook, used by: Integrated Animals, listed by: One Mind Biospecimen Bank ListingLast checked upnif-0000-00242http://zebrafish.org/home/guide.php
CIRCexplorerResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware tool as a combined strategy to identify junction reads from back spliced exons and intron lariats. Computational pipeline to precisely identify junction reads from Circularized Exons. Used to identify circular RNAs (circRNAs and ciRNAs).identify, read, back, spliced, exon, intron, lariat, junction, circularized, circRNA, ciRNASCR_016893(CIRCexplorer, RRID:SCR_016893)CAS, MOST, NSFC, SIBSuses: TopHat, STARPMID:25242744Last checked upSCR_016894http://yanglab.github.io/CIRCexplorer/
RSRefResource, software resource, software application, data processing softwareSoftware for fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy.Fitting, atomic, model, density, map, x ray, crystallography, electron, microscopySCR_017211(RSRef, RRID:SCR_017211)NIGMSPMID:23376441Last checked downhttp://xtal.ohsu.edu/software/rsref/readme.txt
XFSL: An FSL toolboxResource, software resource, software toolkit, data management software, software applicationA set of many useful automation scripts to facilitate the neuroimaging data analysis process. It contains BASH scripts for MRI data management, FSL automation and web application.mri, data managemnet, fsl automation, software toolkitSCR_014181(XFSL: An FSL toolbox, RRID:SCR_014181)uses: FSL, MRIcron, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked uphttp://xfsl.fmri.cn
LSM Image ExaminerResource, software resource, software application, data management softwareSoftware used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area.data management software, image archive, image management, interactive measurementSCR_014344(LSM Image Examiner, RRID:SCR_014344)Last checked downhttp://www.zeiss.com/microscopy/en_us/website/downloads/lsm-image-browser.html http://lsm-image-examiner.software.informer.com
Centre for Reviews and DisseminationResource, institutionA research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance.evidence review, research review, public health, evidence synthesisSCR_010267(Centre for Reviews and Dissemination, RRID:SCR_010267)National Institute for Health Research UKLast checked upnlx_156926http://www.york.ac.uk/
Fungal Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary for the anatomy of fungi.oboSCR_010322(Fungal Gross Anatomy Ontology, RRID:SCR_010322)listed by: BioPortalLast checked upnlx_157409http://www.yeastgenome.org/fungi/fungal_anatomy_ontology/
VectorDB- Molecular Biology Vector Sequence DatabaseResource, data or information resource, databaseA database with information about a variety of vectors, including phage, plasmid, phagemid, phasmid, cosmid, virus and YAC vectors. It also contains information on drosophilia, C. elegans, yeast and drosophilia vectors, including vector functions, hosts and copy number.vector, yeast, phage, plasmid, phagemid, phasmid, cosmid, virus, yac, drosophilia, yeast, flySCR_000745(VectorDB- Molecular Biology Vector Sequence Database, RRID:SCR_000745)Stanford University; Stanford; California Last checked upnif-0000-03625http://www.yeastgenome.org/http://seq.yeastgenome.org/vectordb/
XenbaseResource, database, service resource, storage service resource, atlas, image repository, data repository, data or information resourceData collection for Xenopus laevis and Xenopus tropicalis biology and genomics.molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standardSCR_003280(Xenbase, RRID:SCR_003280)University of Calgary; Alberta; Canada NICHDrelated to: Bgee: a dataBase for Gene Expression Evolution, used by: Monarch Initiative, listed by: OMICtools, One Mind Biospecimen Bank ListingReferences (2)Last checked upnif-0000-01286, OMICS_01665http://www.xenbase.org/entry/
XCEDE SchemaResource, software resource, software application, data management softwareData management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit.computed tomography, eeg, meg, electrocorticography, magnetic resonance, pet, spect, schema, metadata, neuroimaging, clinical neuroinformaticsSCR_002571(XCEDE Schema, RRID:SCR_002571)related to: Human Imaging Database, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_155974http://www.xcede.org/XCEDE.html, http://www.nitrc.org/projects/qa_procedure, http://www.nitrc.org/projects/xcede
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