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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Core Wrapper Resource Report Resource Website 1+ mentions |
Core Wrapper (RRID:SCR_024087) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:09 | 1 | ||||||||
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cyvcf2 Resource Report Resource Website 1+ mentions |
cyvcf2 (RRID:SCR_024000) | software library, software toolkit, software resource | 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 | 2026-08-12 10:52:56 | 2 | |||||||
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NanoLyse Resource Report Resource Website 1+ mentions |
NanoLyse (RRID:SCR_024125) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:04 | 5 | ||||||||
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sumo Resource Report Resource Website 100+ mentions |
sumo (RRID:SCR_001572) | sumo | production service resource, data analysis service, analysis service resource, service resource | Service that searches carbohydrate structures for motifs commonly used for carbohydrate classification, like N- and O-glycan cores, Lewis antigens, etc. Note: Sumo is currently under construction. Motif searches are a frequently used tool in proteomics. For carbohydrate structures, there are also many motifs classified in the literature, e.g. the Lewis antigens or the diverse O-glycan core structures. Sumo is a tool to locate such motifs in a carbohydrate structure given in LINUCS or in IUPAC nomenclature., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | carbohydrate, structure, carbohydrate structure, motif, carbohydrate classification, sugar, iupac, nomenclature, notation |
is related to: LINUCS has parent organization: glycosciences.de |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152885 | SCR_001572 | sumo: SUgar MOtif search, SUgar MOtif search | 2026-08-12 10:48:25 | 215 | |||||||
|
SimpleITK Resource Report Resource Website 50+ mentions |
SimpleITK (RRID:SCR_024693) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:09 | 69 | ||||||
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Four-dimensional Ascidian Body Atlas Resource Report Resource Website 1+ mentions |
Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) | FABA | data or information resource, atlas, d spatial image | Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate. | gene expression, genome, comparative genomics, human, microarray data, model organism, vertebrate, development, ascidian, embryonic development, embryo, video, developmental stage, 3d, slice, timelapse, egg, larva, time, confocal laser scanning microscopy | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD ; Japan Society for the Promotion of Science 18770207 |
PMID:17557317 | Free, Freely Available | nif-0000-02529 | http://ciona.lab.nig.ac.jp/ascidian/top.html | SCR_001691 | FABA: Four-dimensional Ascidian Body Atlas | 2026-08-12 10:48:27 | 5 | |||||
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GeneWiz browser Resource Report Resource Website 1+ mentions |
GeneWiz browser (RRID:SCR_001454) | production service resource, analysis service resource, 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 | 2026-08-12 10:48:24 | 6 | ||||||||
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quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:01 | 12 | ||||||||
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FunDO Resource Report Resource Website 10+ mentions |
FunDO (RRID:SCR_001725) | FunDO | production service resource, data analysis service, analysis service resource, service resource | Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods. | gene, disease, ontology, function |
is related to: KOBAS is related to: Human Disease Ontology has parent organization: Northwestern University; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10225 | SCR_001725 | FunDO - Exploring Genes Using Functional Disease Ontology Annotations | 2026-08-12 10:48:27 | 11 | |||||||
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Cartopy Resource Report Resource Website 1+ mentions |
Cartopy (RRID:SCR_024587) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:16 | 9 | ||||||||||
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bayesplot Resource Report Resource Website 1+ mentions |
bayesplot (RRID:SCR_024588) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:10 | 3 | ||||||||||
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pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:05 | 3 | ||||||||
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HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | production service resource, data analysis service, analysis service resource, service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | 2026-08-12 10:48:27 | 125 | ||||||
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PhenoBank Resource Report Resource Website 1+ mentions |
PhenoBank (RRID:SCR_000930) | data or information resource, video resource, database | 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 | 2026-08-12 10:48:18 | 1 | |||||||||
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RetractionWatch.com Resource Report Resource Website 1+ mentions |
RetractionWatch.com (RRID:SCR_000654) | data or information resource, narrative resource, blog | Retraction Watch is a blog of retractions in the scientific literature. It is maintained by Adam Marcus and Ivan Oransky and has been operating since August 2010. | literature, retraction, bibliographic, database, blog |
is used by: NIF Data Federation is used by: Integrated Blogs |
nif-0000-06675 | SCR_000654 | retractionwatch, Retraction Watch | 2026-08-12 10:48:15 | 4 | |||||||||
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Phevor Resource Report Resource Website 1+ mentions |
Phevor (RRID:SCR_002273) | Phevor | production service resource, data analysis service, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. | genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele | has parent organization: University of Utah School of Medicine; Utah; USA | PMID:24702956 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000139 | SCR_002273 | Phenotype Driven Variant Ontological Re-Ranking Tool | 2026-08-12 10:48:33 | 9 | ||||||
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python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software library, software toolkit, software resource | 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 | 2026-08-12 10:53:01 | 49 | |||||||||
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MADELINE Resource Report Resource Website 1+ mentions |
MADELINE (RRID:SCR_001979) | MADELINE | service resource, software resource, software application | Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. | gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:17488757 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154446, OMICS_00210 | http://eyegene.ophthy.med.umich.edu/#madeline | SCR_001979 | Madeline | 2026-08-12 10:48:30 | 5 | |||||
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BLASTP Resource Report Resource Website 100+ mentions |
BLASTP (RRID:SCR_001010) | production service resource, data analysis service, analysis service resource, service resource | Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast. | blast, basic local alignment search tool, protein alignment, protein blast, data analysis service, protein |
is used by: Open Reading Frame Finder is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
Freely available, Acknowledgement requested | OMICS_00991 | SCR_001010 | blastp suite, Standard Protein BLAST | 2026-08-12 10:48:19 | 293 | ||||||||
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PLoS Blogs Resource Report Resource Website 1+ mentions |
PLoS Blogs (RRID:SCR_001371) | PLoS Blogs | data or information resource, narrative resource, blog | PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine. | science, medicine, health |
is used by: NIF Data Federation is used by: Integrated Blogs is parent organization of: NeuroTribes is parent organization of: Wordpress ePub Plugin |
Creative Commons Attribution License, 1 has restrictions - see bottom of blogs and abide by restrictions | nif-0000-07759 | SCR_001371 | Public Library of Science - Science Blog Network, PLoS Blogs Network, Public Library of Science Blogs | 2026-08-12 10:48:23 | 2 |
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