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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Zebrafinch Brain Architecture Project Resource Report Resource Website 1+ mentions |
Zebrafinch Brain Architecture Project (RRID:SCR_004277) | Zebrafinch Brain Architecture Project | atlas, data or information resource | Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies. | nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brain | has parent organization: Brain Architecture Project | W. M. Keck Foundation ; Crick-Clay Professorship ; NINDS NS50436; NIGMS R24 GM092842 |
nlx_143663 | SCR_004277 | 2026-09-03 05:01:25 | 5 | ||||||||
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bioPIXIE Resource Report Resource Website 1+ mentions |
bioPIXIE (RRID:SCR_004182) | bioPIXIE | analysis service resource, data analysis service, production service resource, service resource | bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). | prediction, bayesian network, probabilistic, interaction, network | has parent organization: Princeton University; New Jersey; USA | NHGRI T32 HG003284; NIGMS R01 GM071966; NHGRI R01 HG003471; NIGMS P50 GM071508; NSF DGE-9972930; NSF IIS-0513552 |
PMID:16420673 | nlx_20893 | SCR_004182 | biological Process Inference from eXperimental Interaction Evidence | 2026-09-03 05:01:39 | 1 | ||||||
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LIPID MAPS Structure Database Resource Report Resource Website 10+ mentions |
LIPID MAPS Structure Database (RRID:SCR_003817) | LMSD | data or information resource, database | Collection of structures and annotations of biologically relevant lipids that contains unique lipid structures. Structures of lipids from : LIPID MAPS Consortium's core laboratories and partners; lipids identified by LIPID MAPS experiments; biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; novel lipids submitted to peer-reviewed journals; and computationally generated structures for appropriate classes. All the lipid structures adhere to the structure drawing rules proposed by the LIPID MAPS consortium. A number of structure viewing options are offered: gif image (default), Chemdraw (requires Chemdraw ActiveX/Plugin), MarvinView (Java applet) and JMol (Java applet). All lipids have been classified using the LIPID MAPS Lipid Classification System. Each lipid structure has been assigned a LIPID MAPS ID (LM_ID) which reflects its position in the classification hierarchy. In addition to a classification-based retrieval of lipids, users can search using either text-based or structure-based search options. | fatty acyl, glycerolipid, glycerophospholipid, sphingolipid, sterol lipid, prenol lipid, sacccharolipid, polyketide, lipid, structure, image, annotation, metabolomics | has parent organization: LIPID Metabolites And Pathways Strategy | NIGMS | PMID:17098933 | Public, Free, Acknowledgement required, Non-commercial, Copyrighted | nlx_158117 | SCR_003817 | LIPID MAPS Structure Database (LMSD) | 2026-09-03 05:01:36 | 24 | |||||
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PERFect Resource Report Resource Website 1+ mentions |
PERFect (RRID:SCR_024682) | data processing software, software application, software resource | Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. | filtering test, microbiome data, microbiome data processing, | NIGMS 1U54GM104944; NSF |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-09-03 05:00:12 | 1 | ||||||||
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WebProtege Resource Report Resource Website 1+ mentions |
WebProtege (RRID:SCR_024627) | software resource, web application | Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat. | editing biomedical ontologies, editing OWL 2 ontologies, ontology editor, OBO ontologies, |
has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research |
NIGMS GM103316 | PMID:24771560 | Free, Freely available | https://protegewiki.stanford.edu/wiki/WebProtege | SCR_024627 | WebProtégé | 2026-09-03 04:59:40 | 2 | ||||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | data processing software, software application, software resource | Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. | parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit |
is listed by: OMICtools is related to: MUMmer has parent organization: SourceForge has parent organization: University of Maryland; Maryland; USA |
NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-09-03 04:59:45 | 5 | |||||
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Drug Design Data Resource Resource Report Resource Website 1+ mentions |
Drug Design Data Resource (RRID:SCR_000497) | D3R | data or information resource, database, portal | Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms. | computer-aided drug design, drug design, pharmaceutical, small molecule, ligand-protein interaction, protein, ligand, drug development, drug, binding, data set, affinity, computation, medicine, compound, structure |
uses: Binding MOAD uses: Protein Data Bank Bind Database is used by: NIF Data Federation is listed by: DataCite has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIGMS 1U01GM111528 | nlx_158375 | https://api.datacite.org/dois?prefix=10.15782 | SCR_000497 | Drug Design Data (D3R) Resource | 2026-09-03 04:59:43 | 3 | ||||||
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OpenMM Resource Report Resource Website 10+ mentions |
OpenMM (RRID:SCR_000436) | simulation software, software application, software resource, standalone software | Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures. | modeling, molecular dynamics, molecular simulation |
is used by: CHARMM-GUI is listed by: Simtk.org has parent organization: Stanford University; Stanford; California |
NCI P30 CA008748; NIGMS R01 GM062868; NIGMS U54 GM072970 |
PMID:28746339 PMID:23316124 PMID:38154096 DOI:10.1021/acs.jpcb.3c06662 |
Free, Available for download, Freely available | nif-0000-23334 | https://github.com/openmm/openmm, https://openmm.org/, https://openmm.org/documentation, https://github.com/openmm | https://simtk.org/home/openmm | SCR_000436 | OpenMM 8, OpenMM, OpenMM 7, OpenMM 4 | 2026-09-03 05:00:21 | 12 | ||||
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NIGMS Human Genetic Cell Repository Resource Report Resource Website 1+ mentions |
NIGMS Human Genetic Cell Repository (RRID:SCR_004517) | NIGMS Repository | biomaterial supply resource, cell repository, material resource | Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics. | cell, gene, cell line, dna, fibroblast, transformed lymphoblast, lymphoblast, induced pluripotent stem cell line, chromosomal abnormality, healthy, single-gene disorder, complex polygenic disorder, multifactorial birth defect, unaffected first-degree relatives of individuals with genetic disease, heritable disease, genetic disease, human variation, control, clinical data, blood |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines has parent organization: Coriell Cell Repositories |
Chromosomal abnormality, Healthy, Single-gene disorder, Complex polygenic disorder, Multifactorial birth defect, Unaffected first-degree relatives of individuals with genetic disease, Heritable disease, Genetic disease, Control | NIGMS ; NIH Blueprint for Neuroscience Research |
Public / non-commercial: Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, Medical, Educational, Or industrial organizations engaged in biomedical research with Statement of Research Intent and a MTA. Samples obtained from the Repository, And material derived from the samples, May not be used for commercial purposes, Although knowledge gained from their use may be used. | nlx_143798 | SCR_004517 | Human Genetic Cell Repository | 2026-09-03 04:59:36 | 4 | |||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data analysis software, data processing software, software application, software resource | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016297 | , GLIMMPSE Version 3 | 2026-09-03 04:58:27 | 9 | ||||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data analysis software, data analytics software, data processing software, software application, software resource, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI076327; NIAID R01 AI134246; NIAID R01 AI134713; NIAID R21 AI142667; NIAID T32 AI10667; NIAID U19 AI135976; NICHD T32 HD007233; NIGMS T32 GM007270; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-09-03 04:58:28 | 23 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software application, software resource | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-09-03 04:58:36 | 4 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data analysis software, data processing software, software application, software resource | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-09-03 04:58:45 | 20 | |||||||
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ZDOCK Server Resource Report Resource Website 100+ mentions |
ZDOCK Server (RRID:SCR_022518) | data access protocol, software resource, web service | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-09-03 04:58:46 | 137 | |||||||||
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sei Resource Report Resource Website 10+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-09-03 04:58:42 | 10 | ||||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | data access protocol, software resource, web service | Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses. | genomic data integration, support systems biology, genomic data visualization and analysis | FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS 5F32GM75600; NIGMS R01 GM 032877; NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-09-03 04:58:49 | 3 | ||||||||
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Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | data analysis software, data processing software, software application, software resource | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-09-03 04:58:58 | 2 | ||||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO | SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-09-03 04:59:04 | 19 | |||||
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SViCT Resource Report Resource Website 1+ mentions |
SViCT (RRID:SCR_023656) | data analysis software, data processing software, software application, software resource | Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA. | detecting structural variations, cell free DNA, cfDNA, circulating tumor DNA low dilutions, ctDNA | Indiana University Grant Challenges Program ; National Science Foundation ; Natural Sciences and Engineering Research Council Discovery Frontiers Program ; Natural Sciences and Engineering Research Council Discovery Grant ; NIGMS GM108348; Precision Health Initiative ; Terry Fox Research Institute New Frontiers Program Project Grant |
PMID:30759232 | Free, Available for download, Freely available | SCR_023656 | Structural Variant detection in Circulating Tumor DNA | 2026-09-03 04:59:22 | 1 | ||||||||
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CRISPRscan Resource Report Resource Website 50+ mentions |
CRISPRscan (RRID:SCR_023777) | data access protocol, software resource, web service | Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR. | predictive sgRNA-scoring, sequence features capture, affecting Cas9/sgRNA activity in vivo, select gRNAs for CRISPR, | has parent organization: Yale University; Connecticut; USA | Edward Mallinckrodt Jr Foundation ; NICHD R01 HD081379; NICHD R21 HD073768; NIGMS GM081602; NIGMS R01 GM101108; NIGMS R01 GM102251; NIGMS R01 GM103789; Swiss National Science Foundation |
Free, Freely available | SCR_023777 | 2026-09-03 04:59:15 | 85 |
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