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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | workflow software, software application, data processing software, software resource | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/ https://bio.tools/ambergpumdsimulation |
SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-02-15 09:20:56 | 1 | ||||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:50 | 8 | ||||||||
|
MORGAN Resource Report Resource Website 100+ mentions |
MORGAN (RRID:SCR_006906) | MORGAN | software application, software resource | Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. | gene, genetic, genomic, c, unix, compaq-alpha, solaris, linux, linkage disequilibrium, gl_lods, ibd_haplo, identity by descent, segregation, linkage analysis, markov chain monte carlo |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Washington; Seattle; USA |
NIGMS GM-46255 | PMID:22298700 | nlx_154201, OMICS_00205 | SCR_006906 | MOnte caRlo Genetic ANalysis PANGAEA | 2026-02-15 09:19:24 | 305 | ||||||
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PERFect Resource Report Resource Website |
PERFect (RRID:SCR_024682) | software application, data processing software, 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, | NSF ; NIGMS 1U54GM104944 |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-02-15 09:22:46 | 0 | ||||||||
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WebProtege Resource Report Resource Website 1+ mentions |
WebProtege (RRID:SCR_024627) | web application, software resource | 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 | 2026-02-15 09:23:34 | 2 | ||||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | software application, data processing software, 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 |
NLM R01 LM006845; NIGMS R01 GM083873 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-02-15 09:18:03 | 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 | 2026-02-15 09:17:56 | 3 | ||||||
|
OpenMM Resource Report Resource Website 10+ mentions |
OpenMM (RRID:SCR_000436) | software application, simulation software, standalone software, software resource | 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 |
NIGMS U54 GM072970; NIGMS R01 GM062868; NCI P30 CA008748 |
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 | 2026-02-15 09:17:55 | 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 | material resource, cell repository, biomaterial supply 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 | 2026-02-15 09:18:49 | 4 | |||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-02-15 09:17:55 | 1 | ||||||
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Integrative Modeling Platform Resource Report Resource Website 50+ mentions |
Integrative Modeling Platform (RRID:SCR_002982) | IMP | software toolkit, software resource | An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. Its broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. It can also be used from the Chimera molecular modeling system, or via one of several web applications. | integrative modeling, structure determination, hybrid modeling, macromolecular assembly, c++, python, peptide, biomolecule, model, structural characterization, structure |
is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA |
NIGMS R01 GM083960 | PMID:22272186 | GNU Lesser General Public License, v2.1 or later, Acknowledgement requested, GNU General Public License | SciRes_000187 | SCR_002982 | IMP - the Integrative Modeling Platform, Integrative Modeling Platform (IMP), IMP the Integrative Modeling Platform | 2026-02-15 09:18:25 | 54 | |||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | software application, data processing software, software resource, data analytics software, software toolkit, data analysis software | 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 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-02-15 09:22:31 | 22 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | software application, data visualization software, data processing software, 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 | 2026-02-15 09:22:10 | 4 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | software application, data processing software, data analysis software, 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 | 2026-02-15 09:22:18 | 15 | |||||||
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Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:22:52 | 2 | ||||||||
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ZDOCK Server Resource Report Resource Website 50+ mentions |
ZDOCK Server (RRID:SCR_022518) | web service, data access protocol, software resource | 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 | 2026-02-15 09:22:47 | 75 | |||||||||
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sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | web service, data access protocol, software resource | 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 | 2026-02-15 09:22:53 | 6 | ||||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | web service, data access protocol, software resource | 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 | NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754; FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS R01 GM 032877; NIGMS 5F32GM75600 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-02-15 09:22:48 | 2 | ||||||||
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SViCT Resource Report Resource Website 1+ mentions |
SViCT (RRID:SCR_023656) | software application, data processing software, data analysis software, 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 | Natural Sciences and Engineering Research Council Discovery Grant ; Terry Fox Research Institute New Frontiers Program Project Grant ; Natural Sciences and Engineering Research Council Discovery Frontiers Program ; National Science Foundation ; NIGMS GM108348; Indiana University Grant Challenges Program ; Precision Health Initiative |
PMID:30759232 | Free, Available for download, Freely available | SCR_023656 | Structural Variant detection in Circulating Tumor DNA | 2026-02-15 09:23:22 | 1 | ||||||||
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CRISPRscan Resource Report Resource Website 50+ mentions |
CRISPRscan (RRID:SCR_023777) | web service, data access protocol, software resource | 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 | Swiss National Science Foundation ; NICHD R21 HD073768; NIGMS R01 GM103789; NIGMS R01 GM102251; NIGMS R01 GM101108; NIGMS GM081602; NICHD R01 HD081379; Edward Mallinckrodt Jr Foundation |
Free, Freely available | SCR_023777 | 2026-02-15 09:23:16 | 58 |
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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 2U24DK097771-09.
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