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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, software resource, data processing software, software application | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool https://bio.tools/limma https://sources.debian.org/src/r-bioc-limma/ |
SCR_010943 | Linear Models for Microarray Data | 2026-02-14 02:02:08 | 24583 | ||||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-02-14 02:02:07 | 5370 | |||||
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pClamp Resource Report Resource Website 5000+ mentions |
pClamp (RRID:SCR_011323) | data processing software, data acquisition software, data analysis software, software application, software resource | Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. | electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, | is listed by: SoftCite | Commercially available | rid_000085 | https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref | SCR_011323 | patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp | 2026-02-14 02:01:58 | 9678 | |||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | data analysis service, production service resource, service resource, analysis service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-02-14 02:06:26 | 3 | |||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 100+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | data analysis service, production service resource, service resource, analysis service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-02-14 02:06:35 | 492 | |||||
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FIVA - Functional Information Viewer and Analyzer Resource Report Resource Website 1+ mentions |
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) | FIVA | software resource, data processing software, software application | Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: MolGen |
Netherlands Organization for Scientific Research ; industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ; Center IOP Genomics ; European Union QLK3-CT-2001-01473 |
PMID:17237043 | Free for academic use | nlx_149245 | SCR_005776 | FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer | 2026-02-14 02:05:26 | 1 | |||||
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GoBean - a Java application for Gene Ontology enrichment analysis Resource Report Resource Website 10+ mentions |
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) | GoBean | software resource, data processing software, software application | GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible | java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Gachon University of Medicine and Science; Incheon; South Korea |
PMID:22360891 | Free for academic use | nlx_149296 | http://neon.gachon.ac.kr/GoBean/ | SCR_005808 | 2026-02-14 02:05:21 | 22 | ||||||
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BRAIN Initiative Resource Report Resource Website 10+ mentions |
BRAIN Initiative (RRID:SCR_006770) | NIH BRAIN Initiative | data or information resource, organization portal, portal | Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts. | brain, connectomics, disorder, cell, neural, circuit, neurotechnology, data, repository, analysis |
uses: Single Cell Portal recommends: Human Neocortical Neurosolver recommends: Brain Gene Expression Analysis toolbox recommends: clusterExperiment recommends: BioWheel recommends: iELVis recommends: Mediation Analysis of Causality under Confounding recommends: MCell recommends: microMS recommends: MIIVsem recommends: MountainSort recommends: Myriads recommends: nelpy recommends: NetPyNE recommends: Neural Ideal recommends: NEURON recommends: Neuron Tools recommends: Neuroscience Gateway recommends: NUTMEG recommends: PetaVision recommends: PyNWB recommends: pyRayleighCuda recommends: ScanImage recommends: Scope recommends: Seizure-Waves recommends: Silver Lab Microscopy Software recommends: StimVision recommends: TReNA recommends: ALICE recommends: BioImage Suite recommends: EyeWire recommends: GIMME recommends: GMA recommends: Homer2 recommends: Brain Image Library recommends: Data Archive BRAIN Initiative recommends: OpenNeuro recommends: Brain Observatory Storage Service and Database (BossDB) recommends: 1000 Functional Connectomes Project recommends: FastProject recommends: Autopatcher recommends: cytoNet recommends: DiffuserCam recommends: gene Expression Analysis Resource recommends: NeMOarchive recommends: Distributed Archives for Neurophysiology Data Integration recommends: NIDA Data Share recommends: HED Tags lists: University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility is related to: Brain Image Library is related to: OpenNeuro is related to: Distributed Archives for Neurophysiology Data Integration is related to: NeMO Analytics is related to: Brainome portal is related to: CEMBA MethylC Seq Pipeline is related to: Seattle Alzheimer Disease Brain Cell Atlas is related to: EBRAINS has parent organization: National Institutes of Health is parent organization of: Data Archive BRAIN Initiative is parent organization of: OpenNeuro is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has organization facet: 3D Developmental Mouse Brain Common Coordinate Framework |
Alzheimer's disease, Schizophrenia, Autism, Epilepsy, Traumatic brain injury | BRAIN Initiative | nlx_155554 | http://braininitiative.nih.gov/ http://www.whitehouse.gov/share/brain-initiative http://en.wikipedia.org/wiki/BRAIN_Initiative |
SCR_006770 | , Brain Research through Advancing Innovative Neurotechnologies Initiative, NIH Brain Research through Advancing Innovative Neurotechnologies Initiative | 2026-02-14 02:05:06 | 18 | |||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software resource, data processing software, software application | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-02-14 02:05:23 | 0 | |||||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | software resource, image analysis software, data processing software, software application | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NIBIB EB025145; NIBIB R01 EB006385; NCRR P41 RR14075 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2 https://homer-fnirs.org/ |
SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2026-02-14 02:05:30 | 223 | ||||||
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DSI Studio Resource Report Resource Website 500+ mentions |
DSI Studio (RRID:SCR_009557) | DSI Studio | software resource, image analysis software, data processing software, software application | A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. | analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
BSD License | nlx_155737 | http://www.nitrc.org/projects/dsistudio | SCR_009557 | 2026-02-14 02:05:09 | 558 | |||||||
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DPABI Resource Report Resource Website 1000+ mentions |
DPABI (RRID:SCR_010501) | DPABI | data processing software, software resource, software toolkit, software application | Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI). | neuroimaging, resting-state fmri, brain, analysis, fmri |
uses: DPARSF has parent organization: RFMRI.ORG |
GNU General Public License | nlx_158469 | SCR_010501 | DPABI: a toolbox for Data Processing & Analysis of Brain Imaging, toolbox for Data Processing and Analysis of Brain Imaging | 2026-02-14 02:05:10 | 1048 | |||||||
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Hunt Biobank Resource Report Resource Website 10+ mentions |
Hunt Biobank (RRID:SCR_010626) | HUNT Biobank | biomaterial supply resource, cell repository, material resource | International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD). | longitudinal study, population, health, environment, whole blood, dna, serum, plasma, urine, rna, cell, buffy coat, na-heparin, blood, medical history, family medical history, adolescent, self-reported questionnaire, structured interview, clinical measurement, buccal smear, analysis, adult, adolescent, aging, FASEB list |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
nlx_57833 | http://www.huntbiosciences.com/default.asp?Valgt=Ja&Mode=Meny&MenyID=41&HovedMenyID=41&Hovedmeny=HUNT+Biobank | SCR_010626 | Nord-Tr��������ndelag health study Biobank, Nord-Trondelag health study, HUNT Databank | 2026-02-14 02:05:28 | 48 | |||||||
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Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | software resource, data processing software, software application | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/ https://pypi.org/project/fbprophet/ |
SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-02-14 02:05:41 | 3 | |||||||
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WinRHIZO Resource Report Resource Website 10+ mentions |
WinRHIZO (RRID:SCR_017120) | software resource, image analysis software, data processing software, software application | Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots. | image, analysis, root, measurement, plant, morphology, topology, color, Regent Instruments Inc. | Available for purchase | SCR_017120 | 2026-02-14 02:05:38 | 11 | |||||||||||
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qMRLab Resource Report Resource Website |
qMRLab (RRID:SCR_016256) | software resource, image analysis software, data processing software, software application | Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models. | mr, image, analysis, simulation, optimize, protocol | Quebec Bio‐Imaging Network QBIN 8436‐0501; Fonds de Recherche du Québec ‐ Nature et Technologies FRQNT 2015‐PR‐182754; Natural Sciences and Engineering Research Council of Canada (NSERC) ; Canadian Institute of Health Research (CIHR) |
Open source, Free, Available for download | SCR_016256 | qMTLab, qMR Lab | 2026-02-14 02:05:39 | 0 | |||||||||
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HMS LINCS Center Resource Report Resource Website 10+ mentions |
HMS LINCS Center (RRID:SCR_016370) | HMS LINCS | data or information resource, organization portal, portal | Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. | LINCS, Program, library, network, cell, signature, analysis, drugs, human, research |
is related to: HMS LINCS Database has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U54 HL127365 | PMID:29199020 | SCR_016370 | LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center | 2026-02-14 02:05:40 | 15 | |||||||
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SGD Resource Report Resource Website 1000+ mentions |
SGD (RRID:SCR_004694) | SGD, SGD LOCUS, SGD REF | data or information resource, database | A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available. | database, yeast, pathway, analysis, gene, nomenclature, predicted sequence, fungi, functional relationship, protein structure, bio.tools, FASEB list |
uses: InterMOD is used by: NIF Data Federation is used by: PhenoGO is listed by: re3data.org is listed by: OMICtools is listed by: InterMOD is listed by: bio.tools is listed by: Debian is affiliated with: InterMOD is related to: AmiGO is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking is related to: HomoloGene is related to: TXTGate is related to: PhenoGO has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford University; Stanford; California is parent organization of: Ascomycete Phenotype Ontology is parent organization of: SGD Gene Ontology Slim Mapper |
NHGRI 5P41HG001315-11; NHGRI 5P41HG002273-05; NHGRI 5U41HG001315-18; NHGRI 2U41HG002273-13; NHGRI 5R01HG004834-04 |
PMID:24265222 PMID:12519985 PMID:9399804 |
Free for academic use, The community can contribute to this resource, Non-commercial | nif-0000-03456, biotools:sgd, r3d100010419, OMICS_01661 | https://bio.tools/sgd https://doi.org/10.17616/R3N313 |
http://genome-www.stanford.edu/Saccharomyces/ | SCR_004694 | SGD LOCUS, Saccharomyces Genome Database, SGD REF | 2026-02-14 02:06:21 | 1920 | |||
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The Guardian: Science Resource Report Resource Website |
The Guardian: Science (RRID:SCR_005166) | Guardian: Science | data or information resource, narrative resource, blog | Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice. | science, news, comment, analysis, space, medicine, genetics, medical research |
is used by: NIF Data Federation is used by: Integrated Blogs |
nlx_144198 | SCR_005166 | 2026-02-14 02:05:51 | 0 | |||||||||
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Scientific American Observations Resource Report Resource Website |
Scientific American Observations (RRID:SCR_005195) | SA Observations | data or information resource, narrative resource, blog | From the editors and reporters of Scientific American, this blog delivers commentary, opinion and analysis on the latest developments in science and technology and their influence on society and policy. From reasoned arguments and cultural critiques to personal and skeptical takes on interesting science news, you''ll find a wide range of scientifically relevant insights here. | commentary, opinion, analysis, science, technology, society, policy |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: Scientific American |
nlx_144201 | SCR_005195 | Scientific American - Observations | 2026-02-14 02:05:55 | 0 |
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