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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
FlexX
 
Resource Report
Resource Website
1+ mentions
FlexX (RRID:SCR_000186) FlexX software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds. protein binding, analysis, ligand, prediction, compounds, screening, protein-ligand docking, is listed by: OMICtools PMID:15382244 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01600 SCR_000186 2026-09-05 06:24:13 5
AS-Peak
 
Resource Report
Resource Website
1+ mentions
AS-Peak (RRID:SCR_000380) ASPeak software resource A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. rna, peak detection, protein, binding, site, algorithm, analysis is listed by: OMICtools
has parent organization: SourceForge
PMID:23929032 Free, Available for download, Freely available OMICS_00566 https://omictools.com/aspeak-tool SCR_000380 2026-09-05 06:24:18 2
LYSIS
 
Resource Report
Resource Website
50+ mentions
LYSIS (RRID:SCR_001385) LYSIS data analysis software, data processing software, simulation software, software application, software resource, software toolkit, source code Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x modeling, data analysis, system modeling, analysis, nonlinear, principal dynamic modes, nonlinear modeling, windows, matlab has parent organization: Biomedical Simulations Resource NIBIB P41-EB001978;
NCRR P41-RR01861
Free, Freely Available nlx_152571 SCR_001385 2026-09-05 06:29:53 56
NeuroExplorer
 
Resource Report
Resource Website
1000+ mentions
NeuroExplorer (RRID:SCR_001818) NeuroExplorer commercial organization, data analysis software, data processing software, software application, software resource Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project neurophysiology, spike train, spike, statistical test, analysis, windows, mac, 3d data, animation, burst analysis, channel, cross correlogram, electrophysiology, matlab, raster analysis, scripting is listed by: 3DVC Free, Available for download, Freely available nlx_158483, nif-0000-10382 http://www.plexon.com/products/neuroexplorer SCR_001818 NeuroExplorer: Neurophysiological Data Analysis Package 2026-09-05 06:29:53 1297
Neuronland: NLMorphologyConverter
 
Resource Report
Resource Website
1+ mentions
Neuronland: NLMorphologyConverter (RRID:SCR_001817) data analysis software, data processing software, data visualization software, rendering software, simulation software, software application, software resource NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand. format, generation, analysis, biological, morphology, neuron, reconstruction, simulation, three-dimensional, visualization Free, Available for download, Freely available nif-0000-10381 SCR_001817 NLMorphologyConverter 2026-09-05 06:29:53 8
ImageJ
 
Resource Report
Resource Website
10000+ mentions
ImageJ (RRID:SCR_003070) data processing software, image analysis software, image processing software, software application, software resource, software toolkit 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. image, data, processing, analysis, datasets, visualization, uses: NeuriteTracer
is used by: Mouse Behavioral Analysis Toolbox
is used by: Focinator
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: SoftCite
is related to: uManager
is related to: Fiji
is related to: NIH Image
is related to: TrakEM2
is related to: BioVoxxel Toolbox
is related to: Golddigger
is related to: Analyze Complex Roots Tool
is related to: Analyze Spheroid Cell Invasion In 3D Matrix
is related to: PyImageJ
has parent organization: Research Services Branch National Institutes of Mental Health
has plug in: Diffusing Tensor Imaging in Java
has plug in: OrientationJ
has plug in: GRatio for ImageJ
has plug in: BioVoxxel Toolbox
has plug in: WormSizer
has plug in: MultiStackReg
has plug in: Iterative Deconvolve 3D
has plug in: Thunder STORM
has plug in: Whisker tracking macro
has plug in: 3D Roi Manager
has plug in: 3D Objects Counter
has plug in: BoneJ
has plug in: QuickFigures
has plug in: ObjectJ
has plug in: ADAPT
has plug in: DHM Utilities
has plug in: Sholl Analysis
has plug in: nTracer
has plug in: IHC Profiler
has plug in: MicrobeJ
has plug in: AccPbFRET
has plug in: RiFRET
has plug in: JaCoP
has plug in: Cell Counter Plugin for ImageJ
has plug in: Puncta Analyzer
has plug in: SpinalJ
has plug in: ColonyArea
works with: Intensity Ratio Nuclei Cytoplasm Tool
works with: 3D ImageJ Suite
works with: Wound Healing Tool
works with: MorphoLibJ
NIGMS RC2 GM092519;
NIH ;
NIMH ;
NINDS ;
the Laboratory for Optical and Computational Instrumentation ;
the Morgridge Institute for Research ;
Wellcome Trust Strategic Award 095931
PMID:22930834
PMID:29187165
DOI:10.1038/nmeth.2089
Free, Available for download, Freely available ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, SCR_003070 Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ 2026-09-05 06:29:56 29025
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D)
 
Resource Report
Resource Website
50+ mentions
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) AMP T2D, T2DKP data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal 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. type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: Consortia-pedia
is listed by: NIDDK Information Network (dkNET)
is related to: Accelerating Medicines Partnership - Alzheimers
is related to: Accelerating Medicines Partnership - Alzheimers
is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus
is related to: Type 1 Diabetes Knowledge Portal
is related to: Common Metabolic Diseases Knowledge Portal
has parent organization: Foundation for the National Institutes of Health
has parent organization: Accelerating Medicines Partnership
Type 2 diabetes, Diabetes Broad Institute ;
Fundacion Carlos Slim ;
NIDDK ;
NIH ;
University of Michigan
Free, Freely available SCR_014533, nlx_157976 http://www.nih.gov/science/amp/type2diabetes.htm SCR_003743 , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes 2026-09-05 06:29:56 83
University of Bergen Computational Biology Unit
 
Resource Report
Resource Website
1+ mentions
University of Bergen Computational Biology Unit (RRID:SCR_002970) UiB CBU data or information resource, department portal, organization portal, portal An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses. computational, biology, bioinformatics, analysis, structure, molecular, evolution, genome, annotation, functional genomic, programming, rna, dna, molecular biology, protein modelling, integrated genomics, evolutionary genomics has parent organization: University of Bergen; Bergen; Norway Research Council of Norway ;
FUGE programme
nif-0000-30147 http://www.cbu.uib.no SCR_002970 UiB Computational Biology Unit 2026-09-05 06:29:56 1
MetaMorph Microscopy Automation and Image Analysis Software
 
Resource Report
Resource Website
5000+ mentions
MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) MetaMorph data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression. automated, microscope, acquisition, device, control, image, analysis, fluorescent, cell, signaling, counting, protein, expression, Molecular Devices PMID:18367250 Commercially available SciRes_000136 SCR_002368 MetaMorph version 7.8.0.0, Molecular Devices Metamorph Premier Software, MetaMorph image analysis software, MetaMorph Microscopy Automation and Image Analysis Software 2026-09-05 06:29:54 8382
GeneMerge
 
Resource Report
Resource Website
10+ mentions
GeneMerge (RRID:SCR_005744) GeneMerge analysis service resource, data analysis service, production service resource, service resource, software application, software resource THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Harvard University; Cambridge; United States
PMID:12724301 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149203 http://genemerge.cbcb.umd.edu/ SCR_005744 2026-09-05 06:29:59 26
Synapse
 
Resource Report
Resource Website
1000+ mentions
Synapse (RRID:SCR_006307) Synapse data or information resource, data repository, database, service resource, storage service resource A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list is used by: NF Data Portal
is listed by: FORCE11
is listed by: DataCite
is listed by: re3data.org
is related to: clearScience
is related to: Exemplar Microscopy Images of Tissues
has parent organization: Sage Bionetworks
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome Life Sciences Discovery Fund ;
NCI ;
NHLBI ;
Alfred P. Sloan Foundation
The community can contribute to this resource nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 SCR_006307 2026-09-05 06:30:00 1104
Clair library
 
Resource Report
Resource Website
Clair library (RRID:SCR_007019) Clairlib data analysis software, data processing software, software application, software resource, software toolkit, text extraction software, text-mining software A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries. analysis, information, linguistic, module, network, process, retrieval, perl, natural language processing, information retrieval, network analysis is listed by: Biositemaps
has parent organization: University of Michigan; Ann Arbor; USA
NSF IIS 0534323;
NSF IIS 0329043;
NSF BCS 0527513;
NLM R01 LM008106;
NIDA U54 DA021519
Open unspecified license: Content is available under GNU Free Documentation License 1.3 or later. nif-0000-33210 SCR_007019 Computational Linguistics And Information Retrieval Library 2026-09-05 06:30:00 0
GIMME
 
Resource Report
Resource Website
1+ mentions
GIMME (RRID:SCR_014115) GIMME data analysis software, data processing software, software application, software resource, software toolkit Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. Functional, connectivity, analysis, fMRI, BOLD, signal, predefined, region, pattern, BRAIN Initiative uses: MATLAB
is recommended by: BRAIN Initiative
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Pennsylvania; Philadelphia; USA
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
NIBIB EB022904;
NIBIB R21 EB015573;
NSF 0852147
PMID:22732562 Free, Available for download, Freely available SCR_014115 Group Iterative Multiple Model Estimation 2026-09-05 06:30:05 2
DESeq2
 
Resource Report
Resource Website
10000+ mentions
DESeq2 (RRID:SCR_015687) data analysis software, data processing software, software application, software resource, software tool Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools is used by: Glimma
is used by: TEtranscripts
is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: SARTools
works with: tximport
European Union’s 7th Framework Programme ;
International Max Planck Research School for Computational Biology and Scientific Computing ;
NCI T32 CA009337
Free, Available for download, Freely available biotools:deseq2 https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 SCR_015687 2026-09-05 06:30:06 50789
Pipeline Pilot
 
Resource Report
Resource Website
100+ mentions
Pipeline Pilot (RRID:SCR_014917) data analysis software, data processing software, software application, software resource Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results. automation, accessing, analysis, analyzing, scientific data, aggregation. aggregate, research, scientific is listed by: SoftCite Commercial SCR_014917 2026-09-05 06:30:06 358
Pilon
 
Resource Report
Resource Website
1000+ mentions
Pilon (RRID:SCR_014731) data analysis software, data processing software, sequence analysis software, software application, software resource 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. automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
is related to: shovill
is hosted by: GitHub
DOI:10.1371/journal.pone.0112963
DOI:10.1371/journal.pone.0112963
Available for download, Acknowledgement requested OMICS_14553, biotools:pilon https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ SCR_014731 2026-09-05 06:30:06 3377
Brain Imaging Analysis Kit
 
Resource Report
Resource Website
10+ mentions
Brain Imaging Analysis Kit (RRID:SCR_014824) BrainIAK data processing software, image analysis software, software application, software resource, software toolkit Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data. brain, python, module, imaging, fmri, data, analysis, neuroimaging is related to: Intel
has parent organization: Princeton University; New Jersey; USA
Free, Available for download, Freely available https://github.com/brainiak/brainiak SCR_014824 BrainIAK, Brain Imaging Analysis Kit, Brain Imaging Analysis Kit (BrainIAK) 2026-09-05 06:30:06 30
Roary
 
Resource Report
Resource Website
500+ mentions
Roary (RRID:SCR_018172) data analysis software, data processing software, sequence analysis software, software application, software resource Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
works with: Scoary
Wellcome Trust PMID:26198102 Free, Available for download, Freely available OMICS_09491, biotools:roary https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ SCR_018172 2026-09-05 06:30:09 710
StringTie
 
Resource Report
Resource Website
1000+ mentions
StringTie (RRID:SCR_016323) data analysis software, data processing software, sequence analysis software, software application, software resource Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
NCI R01 CA120185;
NCI R01 CA134292;
NHGRI R01 HG006102;
NHGRI R01 HG006677;
NIGMS R01 GM105705;
the Cancer Prevention and Research Institute of Texas
PMID:25690850
DOI:10.1038/nbt.3122
Open source, Free, Freely available, Available for download biotools:stringtie, OMICS_07226 https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ SCR_016323 2026-09-05 06:30:07 4976
MrDiffusion
 
Resource Report
Resource Website
1+ mentions
MrDiffusion (RRID:SCR_016567) data analysis software, data processing software, data visualization software, image analysis software, software application, software resource Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. diffusion, imaging, analysis, visualization, data, fractional, anisotropy, MRI is related to: MATLAB
has parent organization: Stanford University; Stanford; California
THIS RESOURCE IS NO LONGER IN SERVICE https://github.com/vistalab/vistasoft/tree/master/mrDiffusion SCR_016567 2026-09-05 06:30:07 9

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