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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Semi-Manual Alignment to Reference Templates Resource Report Resource Website 1000+ mentions |
Semi-Manual Alignment to Reference Templates (RRID:SCR_019265) | SMART | data processing software, image analysis software, segmentation software, software application, software resource | Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets. | Segmenting experimental images, registering experimental images, Allen Mouse Common Coordinate Framework, data processing, experimental images |
is used by: BICCN is related to: Allen Institute for Brain Science |
DOI:10.1101/727529 | Free, Available for download, Freely available | https://mjin1812.github.io/SMART/installation.html | SCR_019265 | 2026-09-05 06:28:48 | 2818 | |||||||
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EBRAINS Resource Report Resource Website 50+ mentions |
EBRAINS (RRID:SCR_019260) | data or information resource, data repository, portal, project portal, service resource, storage service resource | Research infrastructure for the EU Human Brain Project. Provides digital tools and services which can be used to address challenges in brain research and brain inspired technology development. Digital research infrastructure, created by EU-funded Human Brain Project, that gathers extensive range of data and tools for brain-related research. EBRAINS will capitalize on the work performed by the Human Brain Project teams in digital neuroscience, brain medicine, and brain-inspired technology.You can share your neuroscience data, models and software. | EU Human Brain Project, European Union Human Brain Project, human brain project, human brain, OpenMINDs, FAIR |
lists: QuickNII and VisuAlign lists: QuickNII is listed by: FAIRsharing is related to: openMINDS metadata framework is related to: Julich-Brain Cytoarchitectonic Atlas is related to: BRAIN Initiative is related to: openMINDS chemicals metadata model is related to: openMINDS computation metadata model is related to: openMINDS specimenPrep metadata model is related to: openMINDS core metadata model is related to: openMINDS controlledTerms metadata model is related to: openMINDS publications metadata model is related to: openMINDS stimulation metadata model |
EU | Free, Freely available | r3d100013325 | https://doi.org/10.17616/R31NJMRX | SCR_019260 | ebrains, Ebrains | 2026-09-05 06:28:48 | 78 | ||||||
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EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software Resource Report Resource Website 1+ mentions |
EIDORS:Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software (RRID:SCR_019262) | EIDORS | data processing software, image analysis software, image reconstruction software, software application, software resource | Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields. | Modelling, inverse modelling, forward modelling, Electrical Impedance Tomography, Diffusion based Optical Tomography, share data | Free, Available for download, Freely available | SCR_019262 | 2026-09-05 06:28:48 | 4 | ||||||||||
|
National Collaborative on Childhood Obesity Research Resource Report Resource Website 1+ mentions |
National Collaborative on Childhood Obesity Research (RRID:SCR_019150) | NCCOR | data or information resource, disease-related portal, organization portal, portal, topical portal | Brings together Centers for Disease Control and Prevention, National Institutes of Health, Robert Wood Johnson Foundation, and U.S. Department of Agriculture to accelerate progress in reducing childhood obesity in America, to manage projects and reach common goals, to coordinate funding to make the most of available resources, to share insights and expertise to strengthen research. NCCOR focuses on efforts that have to benefit children, teens, and their families, and communities in which they live. | Childhood obesity, reducing childhood obesity, coordinate funding, coordinate projects, benefit children | Obesity | Free, Freely available | SCR_019150 | 2026-09-05 06:28:46 | 1 | |||||||||
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CMGUI Resource Report Resource Website |
CMGUI (RRID:SCR_019271) | 3d visualization software, data processing software, data visualization software, software application, software resource, software toolkit, standalone software | Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs. | 3D visualisation, 3D manipulation, mathematical field models, visualise biomedical images, dynamic geometry fields, cell computer models, tissue computer models, organ computer models, Continuum Mechanics, Imaging, Signal processing, System identification, OpenCMISS | Free, Available for download, Freely available | http://physiomeproject.org/software/opencmiss/cmgui/download | SCR_019271 | Cmgui, Cmgui v3.0 | 2026-09-05 06:28:48 | 0 | |||||||||
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DeePhage Resource Report Resource Website 1+ mentions |
DeePhage (RRID:SCR_019243) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments. | Metavirome data, identify virome sequences, derived fragment, distinguish phage derived sequences, temperate phage sequences, virulent phage sequences, deep learning | https://github.com/shufangwu/DeePhage | SCR_019243 | 2026-09-05 06:28:47 | 4 | |||||||||||
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Fruit Fly Brain Observatory Resource Report Resource Website 1+ mentions |
Fruit Fly Brain Observatory (RRID:SCR_019244) | FFBO | data or information resource, data processing software, data repository, portal, service resource, software application, software resource, storage service resource, topical portal | Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution. | Fruit fly brain function, neural circuits, fly brain data, brain function data, neuron location, neuron morphology, neuron biophysical properties, genetic data, | human neurological and psychiatric disorders, Epilepsy, Parkinson | Free, Freely available | SCR_019244 | 2026-09-05 06:28:48 | 3 | |||||||||
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PhyloPic Resource Report Resource Website 500+ mentions |
PhyloPic (RRID:SCR_019139) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like. | Silhouette images, phylogenetic taxonomy, taxonomic name, taxon ancestral member, supertaxa, subtaxa, image related taxa, FASEB list | Free, Freely available | SCR_019139 | 2026-09-05 06:28:46 | 714 | |||||||||||
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ScanNeo Resource Report Resource Website 1+ mentions |
ScanNeo (RRID:SCR_019253) | data analysis software, data processing software, sequence analysis software, software application, software resource | Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data. | RNA-Seq, neoepitopes, indel, indel derived neoantigen, RNA-Seq data, neoantigen identification | PMID:30887025 | Free, Available for download, Freely available | SCR_019253 | 2026-09-05 06:28:48 | 4 | ||||||||||
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Interact Resource Report Resource Website 1+ mentions |
Interact (RRID:SCR_019254) | software resource | Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software. | Synchronized viewing, analysis, video footage, audio files, observational research, video coding | Restricted | SCR_019254 | 2026-09-05 06:28:48 | 5 | |||||||||||
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BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | data analysis software, data processing software, software application, software resource | Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data. | Biosynthetic Gene, gene clusters, super linear clustering, clustering data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Graduate School for Experimental Plant Sciences Netherlands ; Netherlands eScience Center Accelerating Scientific Discoveries Grant |
DOI:10.1101/2020.08.17.240838 | Free, Available for download, Freely available | biotools:big_slice | https://bio.tools/big_slice | SCR_019130 | Biosynthetic Gene clusters - Super Linear Clustering Engine | 2026-09-05 06:28:46 | 6 | |||||
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cthist Resource Report Resource Website 1+ mentions |
cthist (RRID:SCR_019229) | software resource | Software tool for mass downloading of historical clinical trial data from ClinicalTrials.gov. | Mass downloading, historical clinical trial data, ClinicalTrials.gov, trial registry number | is related to: ClinicalTrials.gov | Free, Available for download, Freely available | https://github.com/bgcarlisle/cthist | SCR_019229 | 2026-09-05 06:28:47 | 2 | |||||||||
|
igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | data analysis software, data processing software, data visualization software, network analysis software, network graph visualization software, software application, software resource, software toolkit | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/, https://github.com/igraph/igraph/releases/tag/0.8.4 | SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-09-05 06:28:47 | 432 | ||||||||
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COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings. | COVID-19, impact data, novel coronavirus global pandemic, novel coronavirus, data |
uses: DataCite is related to: OpenICPSR has parent organization: University of Michigan; Ann Arbor; USA |
COVID-19 | Free, Freely available | https://doi.org/10.3886, https://dx.doi.org/10.3886 | SCR_019105 | 2026-09-05 06:28:46 | 1 | ||||||||
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Authentication Reports Resource Report Resource Website |
Authentication Reports (RRID:SCR_019226) | data access protocol, software resource, web service | dkNET service that assists researchers in preparing authentication plans for cell lines or antibodies to comply with NIH Submission Policy when submitting proposal or publication. Automated tool to enable researchers to create customized report based on key biological resources they plan to use. These customized reports provide additional information such as known problems with particular cell line or antibody. | dkNET Authentication Report, preparing cell lines authentication plans, preparing antibodies authentication plans, NIH Submission Policy, proposal submitting, publication submitting, customized report creation | Free, Freely available | SCR_019226 | 2026-09-05 06:28:47 | 0 | |||||||||||
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Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-09-05 06:28:47 | 5 | ||||||||
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NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | data or information resource, portal, topical portal | Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource. | Human electrophysiological data, neuroelectromagnetic data, neuroelectromagnetic tools, data archives, data analysis, data visualization, EEG data, MEG data, iEEG data, ECoG data, brain data | is affiliated with: OpenNeuro | NIH | Free, Freely available | SCR_019100 | NEuroelectroMagnetic data Archive and tools Resource | 2026-09-05 06:28:46 | 9 | ||||||||
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epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | simulation software, software application, software resource | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/, https://bio.tools/epitopepredict | SCR_019221 | 2026-09-05 06:28:47 | 2 | ||||||||
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CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data access protocol, data processing software, data visualization software, software application, software resource, web service | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | NCI CA102310; NCI CA107263; NCI CA177519; NCI CA207729; NCI P30 CA138313; NIA AG033082; NIGMS GM132055; Nine Girls Ask Foundation |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-09-05 06:28:46 | 0 | |||||||
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ABF Utility Resource Report Resource Website 1+ mentions |
ABF Utility (RRID:SCR_019222) | data analysis software, data processing software, software application, software resource | Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program. | Convert data file, ABF format, data file, data format | Restricted | SCR_019224 | SCR_019222 | 2026-09-05 06:28:47 | 4 |
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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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