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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: Sep 14, 2019)

Physical Resource or Software Tool Software

523 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
bam2wigResource, software resource, software applicationA script to convert Bam alignments into a wig representation file.SCR_015697(bam2wig, RRID:SCR_015697)submitted by: Resource Identification PortalLast checked down
EcoCyte BioscienceResource, service resource, material service resource, production service resourceSupplier and servicer of products for experiments involving Xenopus laevis. Their products include laboratory equipment, media, and oocytes, and their services for pharmacological studies include heterologous expression and in vitro electrophysiology.supplier, commercial, xenopus, xenopus laevis, laboratory equipment, oocyte, pharmacology, heterologous expression, electrophysiologySCR_014773(EcoCyte Bioscience, RRID:SCR_014773)submitted by: Resource Identification PortalLast checked down
X!TandemResource, data analysis software, data processing software, database, software application, software resource, data or information resourceAnalysis software and database that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identificationprotein identification, peptide sequence, tandem mass spectrum, xml fileSCR_015645(X!Tandem, RRID:SCR_015645)submitted by: Resource Identification PortalLast checked down
Oncotopix DiscoveryResource, software resourceOncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.SCR_015690(Oncotopix Discovery, RRID:SCR_015690)submitted by: Resource Identification PortalLast checked down
StatPlus MacResource, software resource, software application, data analysis software, data processing softwareA statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.statistics, mac, ios, excel, data analysis, softwareSCR_014635(StatPlus Mac, RRID:SCR_014635)submitted by: Resource Identification PortalLast checked down
GDAL - Geospatial Data Abstraction Library Resource, software toolA translator library for raster and vector geospatial data formats that presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It includes formats such as GeoTIFF, Erdas Imagine, Arc/Info Binary, CEOS, DTED, GXF, and SDTS. It is intended to provide efficient access suitable for use in viewer applications, and also attempts to preserve coordinate systems and metadata. Python, C, and C++ interfaces are available.software, free software, geospatial, command-line, library_countSCR_014396(GDAL - Geospatial Data Abstraction Library , RRID:SCR_014396)submitted by: Resource Identification PortalDOI:10.1007/978-3-540-74831-1_5Last checked downhttps://directory.fsf.org/wiki/GDAL
Eutherian comparative genomic analysis protocolResource, data set, protocol, data or information resourcePublic eutherian reference genomic sequence data sets ushered in new era in biology and medicine. Nevertheless, future updates and revisions of eutherian gene data sets were expected, due to incompleteness of reference genomic sequence assemblies and potential genomic sequence errors.\\n\\nThe open science research project "Comparative genomic analysis of eutherian genes" established eutherian comparative genomic analysis protocol RRID:SCR_014401 as one framework of updates and revisions of eutherian gene data sets. The protocol included gene annotations, phylogenetic analysis and protein molecular evolution analysis, as well as new test of reliability of public eutherian genomic sequences using genomic sequence redundancies and new test of protein molecular evolution using relative synonymous codon usage statistics.\\n\\nThe protocol was applicable in updates and revisions of 11 major eutherian gene data sets, including 1504 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets under accession numbers: FR734011-FR734074, HF564658-HF564785, HF564786-HF564815, HG328835-HG329089, HG426065-HG426183, HG931734-HG931849, LM644135-LM644234, LN874312-LN874522, LT548096-LT548244, LT631550-LT631670 and LT962964-LT963174. In addition, the protocol curated other eutherian gene data sets (data in preparation).\\n\\nOPEN SCIENCE RESEARCH PROJECT: COMPARATIVE GENOMIC ANALYSIS OF EUTHERIAN GENES\\nPROJECT LEADER: Marko Premzl PhD, The Australian National University Alumni, 4 Kninski trg Sq., Zagreb, Croatia\\nE-MAIL CONTACT ADDRESS: Marko.Premzl@alumni.anu.edu.au\\nNCBI SciENcv: https://www.ncbi.nlm.nih.gov/myncbi/mpremzl/cv/130205/\\nOpen Science Framework Projects: https://osf.io/ax3ts/eutheria, gene, data, set, annotation, genomic, molecular, evolution, phylogenetic, analysis, protocolSCR_014401(Eutherian comparative genomic analysis protocol, RRID:SCR_014401)submitted by: Resource Identification PortalDOI:10.1016/j.dib.2015.11.056, DOI:10.1016/j.genrep.2019.100414Last checked downhttps://doi.org/10.1016/j.genrep.2019.100414
BD Accuri C6 PlusResource, software resource, software application, data analysis software, data processing software, data acquisition softwareSoftware used for collecting and analyzing flow cytometry data. Files can be exported in FCS 3.1 format for import into other flow cytometry analysis programs such as FCS Express™ software and FlowJo™ software.data analysis software, data acquisition software, flow cytometry, flow cytometry analysis programSCR_014422(BD Accuri C6 Plus, RRID:SCR_014422)submitted by: Resource Identification PortalLast checked down
SCiLS LabResource, image analysis software, data analysis software, data processing software, software application, data visualization software, software resourceStatistical software for visualization, analysis and interpretation of MALDI imaging data. Its features are tailored to mining MALDI imaging data and include univariate analysis, unsupervised and supervised multivariate analysis, and preprocessing of data. Tutorials, software trainings, and example data sets can be accessed from the website.univariate analysis, multivariate analysis, imaging data, maldi, proteomics, mass spectrometry, data visualization software, data analysis software, image analysis softwareSCR_014426(SCiLS Lab, RRID:SCR_014426)submitted by: Resource Identification PortalLast checked down
Olympus MicroSuite FiveResource, data processing software, software application, software resource, data acquisition software, image processing software, image acquisition softwareImaging software for monochrome and color image acquisition and processing. It is fully integrated with Olympus microscopes, as well as third party stages and other devices, and supports various CCD and video cameras and TWAIN devices.image acquisition, image analysis, microscope imaging software, system management software, monochrome image, color imageSCR_014425(Olympus MicroSuite Five, RRID:SCR_014425)submitted by: Resource Identification PortalLast checked down
MCID Core Resource, image analysis software, standalone software, data processing software, software application, software resource, data acquisition software, image acquisition softwareA complete imaging software that accepts image files in various formats and serves as a host for phosphor imagers, laser scanners, scanning densitometers and similar devices. Camera support is via compatible digital cameras such as the CoolSNAP or Qimaging range. MCID Core is available as an off the shelf software solution or as part of a number of software/hardware packages optimized for specific applications.image analysis software, phosphor, laser scanner, scanning densitometer, cameraSCR_014419(MCID Core , RRID:SCR_014419)affiliated with: MCID Analysis, submitted by: Resource Identification PortalLast checked down
FlexField SoftwareResource, software resource, software application, standalone software, systems interoperability softwareTransformation software designed to help model and change Oracle account charts. This can be used to reorganize Oracle accounts due to events such as mergers, acquisitions, regulatory requirements and the need for more ranges when the data outgrows the range of the current chart of accounts. FlexField transforms an existing accounting flexfield segment structure, values, code combinations, and CCIDs according to user mappings, and applies the new code combinations and CCIDs. It propagates the change throughout an existing E-Business Suite data, everywhere the accounting flexfield is used. It removes the old code combinations and CCIDs, and aligns the new Chart of Accounts (COA) so that all balances belonging to a single CCID are summarized into a single line.software, oracle, ccid, account chart, segment structure, accounting, chart of accountsSCR_014420(FlexField Software, RRID:SCR_014420)submitted by: Resource Identification PortalLast checked down
WIS-NeuroMathResource, software resource, image analysis software, data processing software, software applicationA software tool for automated analysis and quantification of fluorescent microscopy images of nerve cells in vivo and in vitro. The tool also can be used for analysis of cell morphology, neurite length analysis for sections with no cell body, and ganglion explant analysis.image analysis software, fluorescent microscopy, nerve cell, in vivo, in vitro, cell morphology, neurite, ganglionSCR_014481(WIS-NeuroMath, RRID:SCR_014481)submitted by: Resource Identification PortalPMID:23055261Last checked down
IMAGICResource, software resource, image analysis software, image processing software, data processing software, software applicationAn image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules.image analysis, spectra, multi-dimensional data, macromolecule, 3d processing, tomograph, spectrometer, software environmentSCR_014447(IMAGIC, RRID:SCR_014447)submitted by: Resource Identification PortalPMID:8742718Last checked down
Andor iQResource, software resource, image analysis software, image processing software, data processing software, software applicationA live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis.image acquisition and analysis, iXon, sCMOS, EMCCD, live cell, 3d imageSCR_014461(Andor iQ, RRID:SCR_014461)submitted by: Resource Identification PortalLast checked down
AmplifXResource, software resource, software application, data analysis software, data processing softwareA software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers.primer design, target sequences, amplification, graphic representation, data analysis softwareSCR_014465(AmplifX, RRID:SCR_014465)submitted by: Resource Identification PortalLast checked down
Demon Voltammetry and Analysis SoftwareResource, data analytics software, software application, data processing software, data acquisition software, software resourceA software for performing fast scan cyclic voltammetry recordings in brain tissue for detection of neurotransmitters. It was written in the LabView programming language and can be used to provide command voltage to equipment and record the resulting waveforms. The analysis portion of the software can view and export data, apply noise filters, perform chemometric and waveform kinetic analysis, and create figures.voltammetry, cyclic voltammetry, analysis software, brain tissue, neurotransmitter, tabviewSCR_014468(Demon Voltammetry and Analysis Software, RRID:SCR_014468)NIAAA, NIDAuses: LabView, submitted by: Resource Identification PortalPMID:21392532Last checked down
Proteome DiscovererResource, software resource, software application, workflow software, data processing software, data analysis softwareSoftware for identifying, characterizing, and quantifying proteins in biological samples. It can be used for a range of proteomics workflows such as protein and peptide identification, PTM analysis, and isobaric mass tagging for quantification. It supports multiple database search algorithms and multiple dissociation techniques.data analysis, workflow software, proteomics, database searchSCR_014477(Proteome Discoverer, RRID:SCR_014477)used by: thermo-msf-parser, submitted by: Resource Identification PortalLast checked down
SpikeSort 3DResource, software resource, software application, data analysis software, data processing softwareA software for spike waveform-to-cell classification which can be used both online and offline. The user can identify and isolate clusters/cells using 3D manipulation, as well as calculate waveform parameters like peak, valley, area, and energy.research software, data analysis, spike waveform-to-cell, classification tool, cluster, waveformSCR_014478(SpikeSort 3D, RRID:SCR_014478)submitted by: Resource Identification PortalLast checked down
DNASISResource, software resource, software application, data analysis software, data processing softwareA bioinformatics software for editing, annotating, and analyzing DNA, RNA, and amino acid sequences. It includes analytical tools and can be expanded with homology search, multiple alignment and base calling, and sequence assembly (Phred/Phrap) modules.DNA analysis, bioinformatics analysis, amino acid sequences, homology searchSCR_014488(DNASIS, RRID:SCR_014488)submitted by: Resource Identification PortalLast checked down
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