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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | simulation software, software application, software resource | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim, https://bio.tools/nanosim, https://bio.tools/Trans-NanoSim | SCR_018243 | 2026-08-09 09:07:12 | 21 | ||||||
|
PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | simulation software, software application, software resource | Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST. | Bayesian phylogenetic inference, epidemiological modelling, epidemiological parameter estimation, pathogen phylogeny estimation |
is related to: BEAST2 is related to: BEAST |
NIGMS U01 GM110749; MRC Centre for Global Infectious Disease Analysis |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | 2026-08-09 09:07:36 | 10 | ||||||||
|
missForest Resource Report Resource Website 100+ mentions |
missForest (RRID:SCR_018543) | simulation software, software application, software resource | Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values. | Missing value prediction, mixed type data, non parametric, missing value, mixed data, predictor | is related to: CRAN | PMID:22039212 | Free, Available for download, Freely available | http://stat.ethz.ch/CRAN/ | SCR_018543 | 2026-08-09 09:07:42 | 173 | ||||||||
|
Biorender Resource Report Resource Website 10000+ mentions |
Biorender (RRID:SCR_018361) | web application, service resource, software resource | Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request. | Graphical illustration, biological system, pre made icon, pre made template, scientific illustration, customized icon | Restricted | SCR_018361 | 2026-08-09 09:07:13 | 26474 | |||||||||||
|
robvis Resource Report Resource Website 100+ mentions |
robvis (RRID:SCR_018755) | robvis | web application, software toolkit, software resource | Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project. | Risk of bias assessment, publication figure, publication quality figure, figure production, systematic review, research synthesis project | is related to: Shiny | University of Bristol ; University Hospitals Bristol NHS Foundation Trust |
DOI:10.1002/jrsm.1411 | Free, Freely available | SCR_018755 | Risk Of Bias VISualization | 2026-08-09 09:07:17 | 100 | ||||||
|
OpenCOR Resource Report Resource Website 1+ mentions |
OpenCOR (RRID:SCR_019001) | simulation software, software application, software resource | Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives. | Modeling environment, reproducible science, CellML format model, CellML format model analysis, CellML format model simulation |
uses: Simulation Experiment Description Markup Language is used by: SPARC Portal |
Free, Available for download, Freely available | SCR_019001 | 2026-08-09 09:07:46 | 6 | ||||||||||
|
Fgenesh plus plus Resource Report Resource Website 1+ mentions |
Fgenesh plus plus (RRID:SCR_018928) | simulation software, software application, software resource | Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software. | Automatic gene prediction, eukaryotic genomes, Softberry software, gene finding | is related to: FGENESH Plus | PMID:16925832 | Restricted | SCR_018928 | Fgenesh Plus Plus, FGENESH plus plus, FGENESH Plus Plus | 2026-08-09 09:07:42 | 7 | ||||||||
|
MacroModel Resource Report Resource Website 100+ mentions |
MacroModel (RRID:SCR_016747) | simulation software, software application, software resource | Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex. | molecular, modeling, free, energy, changes, perturbation, method, conformation, motion, interaction, ligand, receptor, complex | has parent organization: Schrodinger | Commercially available, Free version available | https://en.freedownloadmanager.org/Windows-PC/MacroModel.html | SCR_016747 | 2026-08-09 09:07:05 | 138 | |||||||||
|
Shape screening Resource Report Resource Website 1+ mentions |
Shape screening (RRID:SCR_016750) | simulation software, software application, software resource | Software tool for shape-based superposition and similarity searching. Identifies new compounds with shapes (and, if desired, other properties) that are similar to the known binder. | shape, based, superposition, search, new, compound | has parent organization: Schrodinger | Commercially available | SCR_016750 | 2026-08-09 09:07:05 | 3 | ||||||||||
|
PICRUSt Resource Report Resource Website 10+ mentions |
PICRUSt (RRID:SCR_016855) | PICRUSt | simulation software, software application, software resource | Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. | predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA | is related to: PICRUSt2 | Canadian Institutes of Health Research ; Canada Research Chairs program ; Howard Hughes Medical Institute ; NIDDK P01 DK078669; NHGRI U01 HG004866; NHGRI R01 HG004872; Crohn’s and Colitis Foundation of America ; Sloan Foundation ; NHGRI R01 HG005969; NSF CAREER DBI1053486; ARO W911NF1110473 |
PMID:23975157 | Free, Available for download, Freely available | SCR_016856 | SCR_016855 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt | 2026-08-09 09:06:51 | 45 | |||||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | web application, service resource, software resource | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-08-09 09:07:10 | 192 | |||||
|
Neuron Phenotype Ontology Resource Report Resource Website 1+ mentions |
Neuron Phenotype Ontology (RRID:SCR_017403) | NPO | data or information resource, controlled vocabulary, ontology | An ontology for describing the complex phenotypes of neurons. | Cell, type, phenotype, neuron, ontology |
is used by: BICCN is provided by: NIFSTD |
NIMH U24 MH114827; BRAIN Initiative |
Free, Freely available | SCR_017403 | 2026-08-09 09:07:04 | 2 | ||||||||
|
NEURON Resource Report Resource Website 100+ mentions |
NEURON (RRID:SCR_017449) | simulation software, software application, software resource | Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software. | Computational, neurophysiology, model, neuron, network, building, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Yale University; Connecticut; USA |
NIBIB EB022903 | Free, Available for download, Freely available | https://github.com/neuronsimulator/nrn | SCR_017449 | 2026-08-09 09:07:16 | 244 | ||||||||
|
TOYOBO Resource Report Resource Website 1+ mentions |
TOYOBO (RRID:SCR_027440) | commercial organization | Japanese company that began as a textile manufacturer in 1882 and has expanded to become a global provider of high-function products, including films, functional polymers, industrial materials, and biotechnology products such as enzymes and diagnostic reagents. The company's business is organized around its core technologies in polymerization, modification, processing, and biotechnology, allowing it to contribute to fields like healthcare, environment, and electronics. | Japan, polymerization, modification, processing, biotechnology, healthcare, environment, electronics | Crossref Funder ID 100019953, ISNI 0000 0001 2217 1263, GRID grid.471279.e, Wikidata Q7830642 | https://ror.org/020a33943 | SCR_027440 | 2026-08-08 12:08:12 | 6 | ||||||||||
|
Antibody Watch Resource Report Resource Website |
Antibody Watch (RRID:SCR_027424) | knowledge base | Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research. | Text mining antibody specificity, identify potential problems with antibody specificity, identify potential problems, antibody specificity, antibody, scientific literature, | Ministry of Science and Technology ; Taiwan ; NIDDK U24DK097771; NIDA U24DA039832 |
PMID:34043624 | Free, Freely available | SCR_027424 | 2026-08-08 12:08:12 | 0 | |||||||||
|
Revvity: IVIS Spectrum 2 In Vivo Imaging System Resource Report Resource Website 1+ mentions |
Revvity: IVIS Spectrum 2 In Vivo Imaging System (RRID:SCR_027425) | instrument resource | In vivo optical imaging system used in preclinical research to non-invasively monitor and quantify biological processes in living animals over time. Designed with innovative camera with patented coating that delivers high sensitivity 2D and 3D bioluminescence and fluorescence imaging capabilities. | Imaging instrument, in vivo imaging studies, 2D and 3D bioluminescence and fluorescence imaging, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_027425.pdf | Model_Number_IVIS_Spectrum_2 | SCR_027425 | IVIS Spectrum 2 In Vivo Imaging System | 2026-08-08 12:08:01 | 3 | |||||||||
|
BRAINCELL-AID Resource Report Resource Website |
BRAINCELL-AID (RRID:SCR_027398) | web application, software resource | Web service providing annotations for brain cell type–specific marker gene sets derived from single-cell RNA-seq data spanning the entire mouse brain. It uses a multi-agent AI framework that combines fine-tuned large language models with retrieval-augmented generation, producing biologically grounded annotations supported by peer-reviewed literature. | annotations for brain cell type–specific marker gene sets, single-cell RNA-seq data, mouse brain, | is organization facet of: BRAIN Initiative Cell Atlas Network | Free, Freely available, | SCR_027398 | Brain Cell type Annotation and Integration using Distributed AI | 2026-08-08 12:08:07 | 0 | |||||||||
|
Janelia Automatic Animal Behavior Annotator Resource Report Resource Website 1+ mentions |
Janelia Automatic Animal Behavior Annotator (RRID:SCR_027430) | JAABA | web application, software resource | Web application to create variety of automatic behavior classifiers. These classifiers input the animals' trajectories computed by tracking system, and they output time series indicating whether each animal is performing a given behavior in each video frame. Interactive machine learning for automatic annotation of animal behavior. Used to automatically compute interpretable, quantitative statistics describing video of behaving animals. | Automatic behavior classifiers creation, automatic behavior classifiers, automatically compute interpretation, quantitative statistics, describing video of behaving animals, . | PMID:23202433 | Free, Freely available, | SCR_027430 | Janelia Automatic Animal Behavior Annotator (JAABA) | 2026-08-08 12:08:01 | 4 | ||||||||
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ChemDiv Resource Report Resource Website 10+ mentions |
ChemDiv (RRID:SCR_027402) | commercial organization | Target-to-Clinic Contract Research Organization (CRO) headquartered in San Diego, CA USA. ChemDiv executes pre-clinical discovery chemistry and biology for drug development and clinical trials for international portfolio of companies across the entire range of targets with small molecule and biotech drugs. The company operates multiple research and development (R&D) subsidiaries in Russia, Ukraine and China as well as business operations around the world. | drug development, small molecule, biotech drugs, | SCR_027402 | 2026-08-08 12:08:12 | 21 | ||||||||||||
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JEOL: JCM-6000 Benchtop Scanning Electron Microscope Resource Report Resource Website |
JEOL: JCM-6000 Benchtop Scanning Electron Microscope (RRID:SCR_027403) | instrument resource | Compact Benchtop Scanning Electron Microscope. Intuitive operation is achieved via touch panel and new operation screens. The high or low vacuum mode is included in the standard configuration, and EDS can be installed, offering truly multi-functional benchtop SEM. | Jeol, benchtop, scanning electron microscope, microscope | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_027403.pdf | Model_Number_Jeol_JCM-6000 | SCR_027403 | Jeol JCM-6000 | 2026-08-08 12:08:01 | 0 |
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