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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | software toolkit, data processing software, software resource, software application | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-08-11 09:44:11 | 1 | ||||||||
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OpenComet Resource Report Resource Website 50+ mentions |
OpenComet (RRID:SCR_021826) | software application, data processing software, image analysis software, software resource | Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis. | quantify comet parameters, DNA strand breaks, comet assay image analysis | PMID:24624335 | Free, Available for download, Freely available | SCR_021826 | 2026-08-11 09:44:13 | 55 | ||||||||||
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Fred Hutchinson Cancer Center Shared Resources Resource Report Resource Website 1+ mentions |
Fred Hutchinson Cancer Center Shared Resources (RRID:SCR_022607) | data or information resource, portal, organization portal | Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies. | Fred Hutch/University of Washington Cancer Consortium, cancer research services, ABRF, NACCSR |
lists: Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility lists: Fred Hutchinson Cancer Center Antibody Technology Core Facility lists: Fred Hutchinson Cancer Center Cellular Imaging Core Facility lists: Fred Hutchinson Cancer Center Comparative Medicine Core Facility lists: Fred Hutchinson Cancer Center Electron Microscopy Core Facility lists: Fred Hutchinson Cancer Center Experimental Histopathology Core Facility lists: Fred Hutchinson Cancer Center Flow Cytometry Core Facility lists: Fred Hutchinson Cancer Center Hutch Data Core Facility lists: Fred Hutchinson Cancer Center Immune Monitoring Core Facility lists: Fred Hutchinson Cancer Center Preclinical Imaging Core Facility lists: Fred Hutchinson Cancer Center Preclinical Modeling Core Facility lists: Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility lists: Fred Hutchinson Cancer Center Specimen Processing and Research Cell Bank Core Facility lists: Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility lists: Fred Hutchinson Cancer Center Biostatistics Shared Resource |
Free, Freely available | SCR_022607 | 2026-08-11 09:44:25 | 1 | ||||||||||
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Core Wrapper Resource Report Resource Website 1+ mentions |
Core Wrapper (RRID:SCR_024087) | software toolkit, software resource, software library | Software library that exports C++ mmCIF accessors to Python. | exports C++ mmCIF accessors to Python, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/librcsb-core-wrapper0-dev/ | SCR_024087 | CORE-WRAPPER, core-wrapper | 2026-08-11 09:44:46 | 1 | ||||||||
|
cyvcf2 Resource Report Resource Website 1+ mentions |
cyvcf2 (RRID:SCR_024000) | software toolkit, software resource, software library | Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis. | files parsing and querying, VCF files, BCF files, | is listed by: Debian | PMID:28165109 | Free, Available for download, Freely available | OMICS_20006 | https://sources.debian.org/src/cyvcf2/ | SCR_024000 | 2026-08-11 09:44:44 | 2 | |||||||
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NanoLyse Resource Report Resource Website 1+ mentions |
NanoLyse (RRID:SCR_024125) | software toolkit, software resource, software library | Software package to remove reads mapping to the lambda phage genome from a fastq file. | remove reads mapping, lambda phage genome, fastq file, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanolyse/ | SCR_024125 | nanolyse | 2026-08-11 09:44:42 | 5 | ||||||||
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plusTipTracker Resource Report Resource Website 10+ mentions |
plusTipTracker (RRID:SCR_021890) | software application, data processing software, image analysis software, software resource | Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences. | microtubule tracking, microtubule dynamics, microtubule dynamics measurement, plusTIP marker, live cell image sequences | NIGMS U01 GM67230 | PMID:21821130 | Free, Available for download, Freely available | SCR_021890 | 2026-08-11 09:44:14 | 10 | |||||||||
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DeepFly3D Resource Report Resource Website 1+ mentions |
DeepFly3D (RRID:SCR_021402) | software application, data processing software, image analysis software, software resource | Software tool as PyTorch and PyQT5 implementation of 2D-3D tethered Drosophila pose estimation. Image annotation tool used for pose estimation and appendage tracking. Provides interface for pose estimation and to permit further correction of 2D pose estimates, which are automatically converted to 3D pose. | Image annotation, pose tracking, pose estimation, motor circuit, behavioral measure, accurate 3D pose estimation, OpenBehavior |
is listed by: OpenBehavior is related to: DeepFly3D project |
DOI:10.7554/elife.48571 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/deepfly3d/ | SCR_021402 | 2026-08-11 09:44:11 | 1 | ||||||||
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SimpleITK Resource Report Resource Website 50+ mentions |
SimpleITK (RRID:SCR_024693) | software toolkit, software resource, software library | Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms. | multi dimensional image analysis, Insight Segmentation and Registration Toolkit, | is related to: Insight Segmentation and Registration Toolkit | NLM | PMID:24416015 | Free, Available for download, Freely available | https://github.com/SimpleITK/SimpleITK | SCR_024693 | Simple Insight Segmentation and Registration Toolkit | 2026-08-11 09:44:55 | 69 | ||||||
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GeneWiz browser Resource Report Resource Website 1+ mentions |
GeneWiz browser (RRID:SCR_001454) | service resource, analysis service resource, production service resource | An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. | genome, chromosome, alignment, homologous gene, mapping, short sequencing reads, reference chromosome | has parent organization: Technical University of Denmark; Lyngby; Denmark | PMID:21304658 | Free, Freely Available | nif-0000-08429 | SCR_001454 | 2026-08-11 09:40:21 | 6 | ||||||||
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quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software toolkit, software resource, software library | Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments. | Neighbor-Joining algorithm, reconstructing phylogenies from huge alignments, | is listed by: Debian | PMID:3447015 | Free, Available for download, Freely available, | https://sources.debian.org/src/quicktree/ | SCR_024205 | 2026-08-11 09:44:34 | 12 | ||||||||
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Cartopy Resource Report Resource Website 1+ mentions |
Cartopy (RRID:SCR_024587) | software toolkit, software resource, software library | Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support. | geospatial data processing, produce maps production, geospatial data analyses, | Free, Available for download, Freely available | https://scitools.org.uk/cartopy/docs/latest/ | SCR_024587 | 2026-08-11 09:44:54 | 9 | ||||||||||
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bayesplot Resource Report Resource Website 1+ mentions |
bayesplot (RRID:SCR_024588) | software toolkit, software resource, software library | Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow. | Plotting for Bayesian Models, plotting functions, posterior analysis, MCMC diagnostics, prior and posterior predictive checks, | Free, Available for download, Freely available | https://github.com/stan-dev/bayesplot/, https://CRAN.R-project.org/package=bayesplot | SCR_024588 | 2026-08-11 09:44:48 | 3 | ||||||||||
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pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software toolkit, software resource, software library | Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses. | coding psychology experiments, Python | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python-pyepl/ | SCR_024182 | Python Experiment-Programming Library | 2026-08-11 09:44:43 | 3 | ||||||||
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Parsnp Resource Report Resource Website 50+ mentions |
Parsnp (RRID:SCR_024153) | software toolkit, software resource, software library | Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. | align core genome, bacterial genomes, | is listed by: Debian | PMID:25410596 | Free, Available for download, Freely available, | OMICS_21461 | https://sources.debian.org/src/parsnp/, https://github.com/marbl/parsnp | SCR_024153 | parsnp | 2026-08-11 09:44:33 | 54 | ||||||
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PDB2PQR Resource Report Resource Website 1+ mentions |
PDB2PQR (RRID:SCR_024155) | software toolkit, software resource, software library | Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files. | interface for running PDB2PQR web service, prepare structures for further calculations, reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, generating PQR files, | is listed by: Debian | PMID:17488841 | Free, Available for download, Freely available, | OMICS_14370 | https://sources.debian.org/src/pdb2pqr/ | SCR_024155 | pdb2pqr | 2026-08-11 09:44:43 | 2 | ||||||
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PfTools Resource Report Resource Website 1+ mentions |
PfTools (RRID:SCR_024158) | software toolkit, software resource, software library | Software suite of tools to build and search generalized profiles. | build and search generalized profiles, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29588 | https://sources.debian.org/src/pftools/ | SCR_024158 | pftools | 2026-08-11 09:44:43 | 3 | |||||||
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PhySamp Resource Report Resource Website 1+ mentions |
PhySamp (RRID:SCR_024159) | software toolkit, software resource, software library | Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree. | phylogenetic sampling, sample sequence alignment, corresponding phylogenetic tree, | is listed by: Debian | PMID:26055961 | Free, Available for download, Freely available, | OMICS_21686 | https://sources.debian.org/src/physamp/ | SCR_024159 | physamp | 2026-08-11 09:44:33 | 1 | ||||||
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PhenoBank Resource Report Resource Website 1+ mentions |
PhenoBank (RRID:SCR_000930) | data or information resource, database, video resource | A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens. | phenotype, data, c elegans, genome, embryo, gonad, morphology, classification | has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_73232 | SCR_000930 | 2026-08-11 09:40:14 | 1 | |||||||||
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python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software toolkit, software resource, software library | Software Python library and associated set of scripts for rapid implementation of genome scale analyses. | rapid implementation of genome scale analyses, | is listed by: Debian | OMICS_18239 | https://sources.debian.org/src/python3-bx/ | SCR_024202 | 2026-08-11 09:44:34 | 49 |
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