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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Swami: The Next Generation Biology Workbench Resource Report Resource Website 1+ mentions |
Swami: The Next Generation Biology Workbench (RRID:SCR_007217) | NGBW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release. | has parent organization: University of California at San Diego; California; USA | IBM Corporation ; Microsoft Research ; NIGMS 5R01GM073931 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_14257 | http://www.ngbw.org/ | SCR_007217 | Next Generation Biology Workbench, Swami | 2026-02-07 02:07:19 | 2 | ||||||
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nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software resource, software application | Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. | Jupyter, notebook, extension, docker, container, code, computing, environment, data | is related to: University of Washington; Seattle; USA | NHLBI U54 HL127624; NIGMS R01 GM126019; Institute of Technology at University of Washington Tacoma |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | 2026-02-07 02:14:45 | 0 | |||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software resource, software application | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NSF III1755761; NIGMS R01GM113952; NIDA DK097771 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-02-07 02:14:54 | 1 | ||||||||
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MORGAN Resource Report Resource Website 100+ mentions |
MORGAN (RRID:SCR_006906) | MORGAN | software resource, software application | 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 | 2026-02-07 02:14:14 | 297 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software resource, software application | 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 | 2026-02-07 02:14:26 | 1 | ||||||
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AutoDockTools Resource Report Resource Website 1000+ mentions |
AutoDockTools (RRID:SCR_026401) | ADT | software resource, software application | Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. | automated docking, selective receptor flexibility, predict binding, bind to receptor of known 3D structure, ligand, analyze dockings | NIGMS RO1 GM069832 | PMID:19399780 | Free, Available for download, Freely available | https://autodock.scripps.edu/ | SCR_026401 | AutoDockTools: the Graphical User Interface for AutoDock | 2026-02-07 02:17:16 | 1486 | ||||||
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NIGMS - YouTube Resource Report Resource Website |
NIGMS - YouTube (RRID:SCR_005678) | NIGMS - YouTube | video resource, data or information resource | YouTube videos provided by the National Institute of General Medical Sciences (NIGMS). | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149378 | SCR_005678 | National Institute of General Medical Sciences - YouTube | 2026-02-08 09:19:00 | 0 | ||||||||
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Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | data visualization software, software resource, software application, data processing software | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-02-10 09:55:12 | 211 | |||||||
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PERFect Resource Report Resource Website |
PERFect (RRID:SCR_024682) | software resource, software application, data processing software | 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 | 2026-02-10 09:58:47 | 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 | 2026-02-10 09:58:52 | 2 | ||||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | software resource, software application, data processing software | 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 | 2026-02-10 09:54:28 | 5 | |||||
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Zebrafinch Brain Architecture Project Resource Report Resource Website 1+ mentions |
Zebrafinch Brain Architecture Project (RRID:SCR_004277) | Zebrafinch Brain Architecture Project | atlas, data or information resource | Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies. | nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brain | has parent organization: Brain Architecture Project | W. M. Keck Foundation ; Crick-Clay Professorship ; NINDS NS50436; NIGMS R24 GM092842 |
nlx_143663 | SCR_004277 | 2026-02-10 09:55:03 | 4 | ||||||||
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arcasHLA Resource Report Resource Website 1+ mentions |
arcasHLA (RRID:SCR_022286) | software resource, software application, data processing software | Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq. | in silico inference of HLA genotypes, RNA-seq data, HLA typing | DARPA ; Phillip A. Sharp award ; NCI U54CA193313; NIGMS R01GM117591 |
PMID:31173059 | Free | SCR_022286 | 2026-02-10 09:58:13 | 8 | |||||||||
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OpenSim Resource Report Resource Website 500+ mentions |
OpenSim (RRID:SCR_002683) | simulation software, software resource, software application | OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI. | muscle-driven simulation, musculoskeletal biomechanics, neuromuscular simulation, modeling software, simulation software |
is related to: Simtk.org is related to: Neuromuscular Models Library has parent organization: Stanford University; Stanford; California |
Simbios ; NIGMS U54 GM072970; DARPA |
Public, Free, Acknowledgement requested | nif-0000-23308 | https://simtk.org/home/opensim http://opensim.stanford.edu/support/index.html |
SCR_002683 | 2026-02-10 09:54:45 | 514 | |||||||
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | workflow software, software resource, software application, data processing software | 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 | 2026-02-10 09:56:50 | 1 | ||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data visualization software, software resource, software application, data processing software | 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 | 2026-02-10 09:58:08 | 4 | |||||||||
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ConTrack Resource Report Resource Website 10+ mentions |
ConTrack (RRID:SCR_002681) | ConTrack | image processing software, software resource, software application, data processing software | An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo. | diffusion tensor imaging, tractography, brain connectivity, mri, software, source code, pathway, fiber tractography, tissue analysis |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; NIGMS U54 GM072970; NEI EY015000 |
PMID:18831651 | Free, Available for download, Freely available | nif-0000-23303 | SCR_002681 | Connectivity Tracking, Connectivity Tracking (ConTrack) | 2026-02-10 09:54:45 | 13 | |||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software resource, software application | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-02-10 09:56:58 | 11 | ||||||
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SimTKCore Resource Report Resource Website |
SimTKCore (RRID:SCR_008268) | SimTKCore | simulation software, software resource, software application | SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications. | computational algorithm, high-performance, linear algebra, numerical integration, numerical method, optimization, monte carlo sampling, multibody dynamics, molecular force field evaluation, nonlinear root finding, optimizing, cpodes, simbody, ipopt, molmodel, mit license, linux, mac os x, windows |
is listed by: Biositemaps has parent organization: Stanford University; Stanford; California has parent organization: Simtk.org |
NIGMS U54 GM072970 | PMID:20107615 | nif-0000-23310 | SCR_008268 | 2026-02-10 09:55:48 | 0 | |||||||
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MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | web application, software resource | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | 2026-02-10 09:56:51 | 6100 |
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