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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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sietraj Resource Report Resource Website 1+ mentions |
sietraj (RRID:SCR_018021) | simulation software, software application, software resource | Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes. | Binding free energy, Amber, MD trajctory, MM-PBSA, virtual alanine mutation, solvated interaction energy, calculation, parameter, protein-ligand complex | Restricted | SCR_018021 | 2026-09-05 06:28:29 | 2 | |||||||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, data processing software, software application, software resource | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-09-05 06:28:27 | 8 | |||||||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data analysis software, data processing software, software application, software resource, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-09-05 06:28:28 | 6 | |||||||||||
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Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | data analysis software, data processing software, software application, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | 2026-09-05 06:28:27 | 2 | ||||||||||
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cytoHubba Resource Report Resource Website 100+ mentions |
cytoHubba (RRID:SCR_017677) | data analysis software, data processing software, network analysis software, software application, software resource | Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above. | Identify, network, subnetwork, topological, algorithm, analyze, protein, interaction, hub, object, intercome | is a plug in for: Cytoscape | Ministry of Science and Technology (MOST) ; Taiwan |
PMID:25521941 | Free, Available for download, Freely available | http://hub.iis.sinica.edu.tw/cytoHubba/ | SCR_017677 | cytoHubba 1.6 | 2026-09-05 06:28:27 | 451 | ||||||
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Digimeter: DS5 Isolated Bipolar Current Stimulator Resource Report Resource Website 1+ mentions |
Digimeter: DS5 Isolated Bipolar Current Stimulator (RRID:SCR_018001) | instrument resource | Stimulator allows computer control of stimulus amplitude and timing parameters. Designed to speed up and enhance human peripheral nerve diagnostics by facilitating semi-automated nerve excitability tests. It also has roles in wider aspects of clinical neurophysiology research, including psychological, vestibular system and nociceptive testing. CE marked medical device under European Medical Device Regulation. | Medical, device, stimulator, computer control, timing parameter, human peripheral nerve, diagnostic, excitability test, clinical neurophysiology | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018001.pdf | https://www.digitimer.com/wp-content/uploads/2019/09/ds5.pdf | SCR_018001 | 2026-09-05 06:28:28 | 1 | ||||||||||
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fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data analysis software, data processing software, software application, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-09-05 06:28:32 | 23 | |||||||
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SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SAVES v5.0, Structure Analysis and Verification Server | 2026-09-05 06:28:33 | 219 | |||||||||
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Umap Resource Report Resource Website 100+ mentions |
Umap (RRID:SCR_018217) | UMAP | data processing software, data visualization software, software application, software resource, software toolkit | Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data. | Dimension reduction technique, data visualization, singel cell data | is listed by: Debian | Free, Available for download, Freely available | https://github.com/lmcinnes/umap, https://sources.debian.org/src/umap-learn/ | SCR_018217 | Uniform Manifold Approximation and Projection | 2026-09-05 06:28:32 | 179 | |||||||
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ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-09-05 06:28:32 | 2 | |||||||
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SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program of China 2016YFD0100801; National Key Research and Development Program of China 2018YFD0100803; National Natural Science Foundation of China 31701415 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/, https://bio.tools/SnpHub | SCR_018177 | 2026-09-05 06:28:32 | 1 | |||||||
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Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | 2026-09-05 06:28:32 | 19 | |||||||
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SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data analysis software, data processing software, software application, software resource | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; European Research Council ; Wellcome Trust |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-09-05 06:28:32 | 3 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | data analysis software, data processing software, software application, software resource | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; European Research Council ; Royal Society ; Wellcome Trust |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-09-05 06:28:32 | 1 | ||||||||
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How many cells Resource Report Resource Website 10+ mentions |
How many cells (RRID:SCR_018184) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for calculating number of cells that must be sampled in order to see at least n cells of each type for single cell genomics experiments. | Calculating cell number, single cell genomic, genomic experiment, cell type number, New York Genome Center, Satija Lab | Free, Freely available | SCR_018184 | Satija Lab: How Many Cells | 2026-09-05 06:28:32 | 22 | ||||||||||
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Blackfynn Discover Resource Report Resource Website 1+ mentions |
Blackfynn Discover (RRID:SCR_018068) | data or information resource, data repository, data set, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. Data repository for scientific data. Open data library to explore neuroscience data for neurodegenerative diseases for which there are no disease modifying treatments. | Neuroscience data, data repository, neurogenerative disease |
is used by: SPARC Portal is related to: Pennsieve Data Management Platform is organization facet of: SPARC Portal |
epilepsy, Parkinson, Alzheimer, neurodegenerative disease | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_018068 | 2026-09-05 06:28:30 | 1 | |||||||||
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BioSpherix: C-Chamber Resource Report Resource Website 1+ mentions |
BioSpherix: C-Chamber (RRID:SCR_018189) | instrument resource | Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series. | Culture chamber, cell culture, BioSpherix, incubator, gas controlled, temperature controlled, instrument, equipment | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018189.pdf | https://biospherix.com/wp-content/uploads/2017/11/Cell-Research-Literature_C-Chamber-Subchamber.pdf | SCR_018189 | C-Chamber, Culture Chamber | 2026-09-05 06:28:32 | 1 | ||||||||
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medRxiv Resource Report Resource Website 100+ mentions |
medRxiv (RRID:SCR_018222) | data or information resource | Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted. | Preprint, health sciences, clinical science, medical science, research articles, posted uncertified information, data, protocol, article | Free, Freely available | SCR_018222 | 2026-09-05 06:28:33 | 319 | |||||||||||
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MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | data analysis software, data processing software, software application, software resource | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | Innovision Systems MaxTRAQ software | 2026-09-05 06:28:32 | 2 | ||||||||||
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Sony biotechnology: SH800S Cell Sorter Resource Report Resource Website 10+ mentions |
Sony biotechnology: SH800S Cell Sorter (RRID:SCR_018066) | instrument resource | Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection. | ABRF, benchtop cell sorter, instrument, Sony Biotechnology, equipment | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018066.pdf | Model_Number_SH800S | https://www.sonybiotechnology.com/wordpress/wp-content/uploads/2016/05/Sony_SH800S.pdf | SCR_018066 | SH800 cell sorter | 2026-09-05 06:28:30 | 20 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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