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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MRI Compatible and Customizable Microdrive Design for Neuroscience Research Resource Report Resource Website 1+ mentions |
MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) | data or information resource, portal, project portal | Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery. | CAD files, microdrive, MRI compatible microdrive, customizable microdrive, 3D printable microdrive, neuroscience research | DOI:10.1523/ENEURO.0495-20.2021 | Free, Freely available | SCR_019247 | 2026-08-13 09:30:37 | 1 | ||||||||||
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Smart-seq2 Single Nucleus Multi Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) | software toolkit, data processing software, software resource, software application | Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix. | snRNAseq data, Smart-seq2 assays, single nucleus, multi sample, WARP repository |
is used by: BICCN has parent organization: Broad Institute has parent organization: Allen Institute has parent organization: University of California at San Diego; California; USA is organization facet of: Terra |
Free, Freely available | https://app.terra.bio/#workspaces/warp-pipelines/Smart-seq2_Single_Nucleus_Muti-Sample | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_single_nucleus_multisample | SCR_021312 | Multi-snSS2, Smart-seq2 Single Nucleus Multi-Sample Pipeline | 2026-08-13 09:30:22 | 2 | |||||||
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CoMSES Net Resource Report Resource Website 1+ mentions |
CoMSES Net (RRID:SCR_017598) | data or information resource, organization portal, portal | Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse. | Develop, share, reuse, computational, model, social, ecological, system, network, repository, citation, digital, preservation, reproducibility, archive | is listed by: DataCite | Restricted | DOI:10.25937 | https://doi.org/10.25937/, https://dx.doi.org/10.25937/ | SCR_017598 | Network for Computational Modeling in Social and Ecological Sciences | 2026-08-13 09:29:45 | 6 | |||||||
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AutoPilot project Resource Report Resource Website 1+ mentions |
AutoPilot project (RRID:SCR_021448) | data or information resource, portal, project portal | Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists. | Running behavioral experiments, automating behavioral experiments, Raspberry Pis, design experiments modules, OpenBehavior |
is listed by: OpenBehavior is related to: AutoPilot has parent organization: University of Oregon; Oregon; USA |
DOI:10.1101/807693 | Free, Freely available | SCR_021448 | AutoPilot | 2026-08-13 09:30:42 | 1 | ||||||||
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Chinese National Compound Library Resource Report Resource Website 1+ mentions |
Chinese National Compound Library (RRID:SCR_018723) | CNCL | data or information resource, organization portal, portal | Library with storage capacity of over million compounds possessing diversified structures. Coupled with this library will be advanced sample handling, information management and quality control systems. As important material and information resource, CNCL will work with both domestic and international stakeholders to promote sustained development of Chinese pharmaceutical industry. | Library, compound library, compound, diversified structure, sample handling, information management, quality control, pharmaceutical industry | SCR_018723 | 2026-08-13 09:30:07 | 1 | |||||||||||
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ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline Resource Report Resource Website 50+ mentions |
ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (RRID:SCR_021323) | software toolkit, data processing software, software resource, software application | Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards. | ChIP-seq pipeline, processing ChIP-seq reads, aligning to reference genome, peak calling, IDR analysis, replicate data, ENCODE standards | PMID:22955991 | Free, Available for download, Freely available | SCR_021323 | 2026-08-13 09:30:40 | 97 | ||||||||||
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SouthernBiotech Resource Report Resource Website 100+ mentions |
SouthernBiotech (RRID:SCR_019250) | material resource, reagent supplier | Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies. | commercial, antibody, reagent, biomedical, research | SCR_019250 | 2026-08-13 09:30:18 | 134 | ||||||||||||
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Leinco Technologies Resource Report Resource Website 1+ mentions |
Leinco Technologies (RRID:SCR_019252) | material resource, reagent supplier | A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products. | commercial, antibody, reagent, biomedical, research, biotechnology, ELISA, recombinant, proteins, life science | SCR_019252 | 2026-08-13 09:30:22 | 2 | ||||||||||||
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QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | image analysis software, data processing software, software resource, software application | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Invest Northern Ireland ; Experimental Cancer Medicine Centre Network ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund ; Friends of the Cancer Centre ; Cancer Research UK Accelerator |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-08-13 09:30:19 | 2084 | ||||||
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Wikidata Resource Report Resource Website 10+ mentions |
Wikidata (RRID:SCR_018492) | data or information resource, portal, project portal | Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects. | Open knowledge base, structured data storage, Wikimedia data, Wikipedia data, Wikivoyage data, Wiktionary data, Wikisource data |
lists: Scholia is related to: Author Disambiguator is related to: Clinical Trials Wiki Loader is related to: ClinWiki is related to: VanderBot is related to: Mix n Match is related to: Scholia is related to: QuickStatements is related to: Wikidata Query Service is related to: Author Disambiguator is related to: TABernacle is related to: OpenRefine is related to: SourceMD |
Free, Freely available | Wikidata_Q2013 | https://www.wikidata.org/wiki/Q2013 | SCR_018492 | 2026-08-13 09:30:13 | 47 | ||||||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | software toolkit, data processing software, software resource, software application | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-08-13 09:29:47 | 37 | |||||||
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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 | 2026-08-13 09:30:40 | 1 | ||||||||
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NEST Initiative Resource Report Resource Website 1+ mentions |
NEST Initiative (RRID:SCR_020978) | data or information resource, organization portal, portal | Incorporated as non-profit member based organization promoting scientfic collaboration in computational neuroscience.Advances computational neuroscience by pushing limits of large scale simulations of biologically realistic neuronal networks. | Computational neuroscience collaboration, member based organization, large scale simulations, biologically realistic neuronal networks | is parent organization of: NEST Simulator | SCR_020978 | Neural Simulation Technology Initiative | 2026-08-13 09:30:24 | 1 | ||||||||||
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BarensLab Mini-Atlas Resource Report Resource Website 1+ mentions |
BarensLab Mini-Atlas (RRID:SCR_021115) | data or information resource, mni atlas, atlas, reference atlas | Phenotypic variation of transcriptomic cell types in mouse motor cortex.Repository contains analysis code and preprocessed data.Data includes exonic and intronic gene counts, extracted electrophysiological features, extracted morphological features and z-profiles. Datasets with recorded at room temperature and recorded at physiological temperature. | Phenotypic variation, transcriptomic cell types, mouse motor cortex, morpho-electric phenotypes, mouse primary motor cortex, analysis code, preprocessed data, exonic gene counts, intronic gene counts, extracted electrophysiological features, extracted morphological features, z-profiles, raw data, cellular taxonomy, neuron, morphological reconstruction | is related to: BICCN | DOI:10.1101/2020.10.19.343129v1 | Free, Freely available | SCR_021115 | 2026-08-13 09:30:39 | 6 | |||||||||
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Smart-seq2 Multi-Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) | software toolkit, data processing software, software resource, software application | The Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) pipeline was developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. | Single cell data, Smart seq2 technology, scRNAseq data, Smart-seq2 assay data, data processing | is related to: Human Cell Atlas | Free, Available for download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_multisample | SCR_018920 | 2026-08-13 09:30:17 | 4 | |||||||||
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BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | software toolkit, software resource, standalone software, software application | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
Wellcome Trust ; NIGMS R01 GM069758 |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | 2026-08-13 09:30:28 | 1 | ||||||||
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DeepFly3D Resource Report Resource Website 1+ mentions |
DeepFly3D (RRID:SCR_021402) | image analysis software, data processing software, software resource, software application | 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 | 2026-08-13 09:30:29 | 1 | ||||||||
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Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, software resource, portal, project portal | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | 2026-08-13 09:30:33 | 1 | ||||||||
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Tissue Studio Resource Report Resource Website 1+ mentions |
Tissue Studio (RRID:SCR_023001) | image analysis software, data processing software, software resource, software application | Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis. | Definiens Inc., detect target regions, immunohistochemistry specimen, distinguishes cells and sub-cellular objects | PMID:30930117 | Restricted | SCR_023001 | Definiens Tissue Studio | 2026-08-13 09:30:57 | 2 | |||||||||
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Neocortical Microcircuit Portal Resource Report Resource Website 1+ mentions |
Neocortical Microcircuit Portal (RRID:SCR_022032) | data or information resource, portal, project portal | Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit. | rat somatosensory cortex, reconstruction process, cellular and synaptic models, microcircuit, microcircuit predicted properties | European Union Seventh Framework Program ; Gatsby Charitable Foundation ; Cajal Blue Brain project ; Ministerio de Economia y Competitividad Spanish Ministry of Education and Science ; EPFL Hebrew University Collaborative Grant ; EPFL |
DOI:10.3389/fncir.2015.00044 | Free, Freely available | SCR_022032 | Blue Brain Neocortical Microcircuit Portal, NMC portal | 2026-08-13 09:30:48 | 5 |
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