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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Assisted Model Building with Energy Refinement (AMBER) Resource Report Resource Website 1000+ mentions |
Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) | AMBER | simulation software, software application, software resource, standalone software | Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website. | molecular simulation, simulation software, software package, molecular dynamics, pmemed, sander, bio.tools |
is listed by: bio.tools is listed by: Debian |
Acknowledgement requested | biotools:amber | https://bio.tools/amber | SCR_014230 | Assisted Model Building with Energy Refinement | 2026-08-21 12:40:14 | 4081 | ||||||
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Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Resource Report Resource Website |
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology (RRID:SCR_015320) | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July,27,2022. Core facility that provides scientific and budgetary oversight for all CCEH activities. This includes training programs, high school summer internships, and and pilot and feasibility program for new projects. | cancer research, administrative support, budgetary oversight, training programs |
is listed by: NIDDK Information Network (dkNET) has parent organization: Fred Hutchinson Cancer Center has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging has organization facet: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank is organization facet of: Hematology Centers |
cancer | NIDDK P30DK056465 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015922 | SCR_015320 | 2026-08-21 12:40:41 | 0 | |||||||
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Small-world Network Analysis and Partitioning Resource Report Resource Website |
Small-world Network Analysis and Partitioning (RRID:SCR_013662) | data processing software, software application, software resource | SNAP (Small-world Network Analysis and Partitioning) is an extensible parallel framework for exploratory analysis and partitioning of large-scale networks. SNAP is implemented in C, uses OpenMP primitives for parallelization, and targets sequential, multicore, and symmetric multiprocessor platforms. Our intent with SNAP is to provide a simple and intuitive interface for network analysis and application design, hiding the parallel programming complexity from the user. In addition to path-based, centrality, and community identification queries on large-scale graphs, we support commonly-used preprocessing kernels and quantitative measures that help understand the global network topology. The latest version of SNAP (0.4) was released in August 2010. Sponsors: This work was supported in part by NSF Grants CAREER CCF-0611589, NSF DBI-0420513, ITR EF/BIO 03-31654, IBM Faculty Fellowship and Microsoft Research grants, NASA grant NP-2005-07-375-HQ, and DARPA Contract NBCH30390004. Keywords: network, analysis, software, graph, traversal, betweenness centrality, community, identification, multicore, | has parent organization: Georgia Institute of Technology; Georgia; USA | nif-0000-00425 | SCR_013662 | SNAP | 2026-08-21 12:39:57 | 0 | ||||||||||
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NIH Metabolomics program Resource Report Resource Website |
NIH Metabolomics program (RRID:SCR_014634) | data or information resource, funding resource, portal | A US national program which supoorts the development of technologies in order to enhance the metabolomics field. It specifically increases the national metabolomics research capacity by supporting five core programs: Training in Metabolomics, Metabolomics Technology Development, Metabolomics Reference Standard Synthesis, Metabolomics Data Sharing and International Collaboration, and Comprehensive Metabolomics Resource Cores. | metabolomics, national program, training, technology, data sharing, collaboration, standard, resource core, portal, funding resource | is listed by: Metabolomics Workbench | Available to the scientific community | SCR_014634 | National Institutes of Health (NIH) Common Fund Metabolomics, NIH Common Fund Metabolomics program | 2026-08-21 12:40:05 | 0 | |||||||||
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PALEOMIX Resource Report Resource Website 50+ mentions |
PALEOMIX (RRID:SCR_015057) | data processing software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing. | hts data, high-throughput sequencing, ancient dna, adna, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:24722405 DOI:10.1038/nprot.2014.063 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paleomix, OMICS_03749 | https://bio.tools/paleomix, https://sources.debian.org/src/paleomix/ | SCR_015057 | 2026-08-21 12:40:33 | 66 | |||||||
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TRACULA Resource Report Resource Website 10+ mentions |
TRACULA (RRID:SCR_013152) | TRACULA | data processing software, software application, software resource | Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. | tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging |
is related to: FreeSurfer has parent organization: Harvard Medical School; Massachusetts; USA |
Aging | NIH Blueprint for Neuroscience Research ; Ellison Medical Foundation ; NIBIB EB008129; NIMH U01-MH093765; NCRR P41-RR14075; NCRR U24-RR021382; NIBIB R01-EB006758; NIA R01-AG022381; National Center for Complementary and Alternative Medicine RC1-AT005728; NINDS R01-NS052585; NINDS R21-NS072652; NINDS R01-NS070963 |
PMID:22016733 | nlx_143919 | SCR_013152 | TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy | 2026-08-21 12:39:56 | 17 | |||||
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BiofilmQuant Resource Report Resource Website |
BiofilmQuant (RRID:SCR_014088) | data processing software, image analysis software, software application, software resource | A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images. | image analysis software, volumetric analysis, biofilm, dental plaque, quantification, qlf image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download, Acknowledgement requested | SCR_014088 | 2026-08-21 12:40:00 | 0 | ||||||||||
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7T Structural MRI scans ATAG Resource Report Resource Website 1+ mentions |
7T Structural MRI scans ATAG (RRID:SCR_014084) | atlas, data or information resource, data set | Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. | 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Available for download | SCR_014084 | 2026-08-21 12:40:00 | 7 | ||||||||||
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Operational Criteria Resource Report Resource Website 10+ mentions |
Operational Criteria (RRID:SCR_013359) | data or information resource, organization portal, portal | The operational criteria OPCRIT checklist for psychotic and affective illness has been designed to facilitate a polydiagnostic approach to mental illness. The package is specifically for the needs of the researcher and is intended to be used by clinicians or investigators trained in clinical research. It is not recommended for use by raters without previous experience in psychopathology and psychiatric diagnosis. Click the Download link below to download Opcrit. This download is compressed zip file which will yield the actual installer files. Open WinopInstallerFiles.zip and when prompted extract the contents to a temporary location. One of the files extracted is Setup.exe. Run this setup file and follow the instructions to install the Opcrit. Depending on your system type and version of Windows, you may need to reboot your system once installation is complete. After installation, you will also need to download and run the installer for the october 2009 update (see below). | nif-0000-31494 | SCR_013359 | OPCRIT | 2026-08-21 12:39:48 | 37 | |||||||||||
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Proteome Analyst Resource Report Resource Website |
Proteome Analyst (RRID:SCR_013807) | PA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins. | web application, proteome analysis, predictions, sub cellular localization, GO molecular functions, tool |
is related to: Proteome Analyst is related to: Proteome Analyst PA-GOSUB has parent organization: University of Alberta; Alberta; Canada |
NSERC ; AICML ; iCORE ; SGI ; Sun Microsystems |
DOI:10.1093/nar/gkh485 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-03236, SCR_007842 | http://webdocs.cs.ualberta.ca/~bioinfo/PA/GOSUB/ | SCR_013807 | Proteome Analyst | 2026-08-21 12:40:08 | 0 | ||||
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Rhinoceros Resource Report Resource Website 100+ mentions |
Rhinoceros (RRID:SCR_014339) | simulation software, software application, software resource, standalone software | 3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products. | 3d, modeling software, standalone software | is listed by: SoftCite | Pay for product | SCR_014339 | Rhino | 2026-08-21 12:40:17 | 311 | |||||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-08-21 12:39:44 | 0 | ||||||||
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CBiS Resource Report Resource Website 10+ mentions |
CBiS (RRID:SCR_013408) | CBiS | data or information resource, organization portal, portal, software resource | It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, science, mathematics, biological science, research, statistics, quantitative biology, conceptual, architechure, biological system, software | has parent organization: Australian National University; Acton; Australia | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30034 | SCR_013408 | Centre for Bioinformation Science, The Centre for Bioinformation Science | 2026-08-21 12:40:08 | 30 | |||||||
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Neuroscience Information Toolbox Resource Report Resource Website 10+ mentions |
Neuroscience Information Toolbox (RRID:SCR_014501) | NIT | data processing software, software application, software resource, software toolkit | A toolkit for EEG-fMRI multimodal fusion and fMRI data preprocessing and analysis. NIT allows users to perform batch processing of fMRI data analysis and data preprocessing based on SPM8, as well as parallel computing for data preprocessing, nuisance signals removal, and FCD and FOCA calculating. Users can also use NIT to calculate functional connectivity density and four dimensional (spatio-temporal) consistency of local neural activities. | foca, four dimensional consistency of local neural activities, software toolkit, eeg, fmri, multimodal fusion, parallel framework, fcd, functional connectivity density | Acknowledgement requested, Non-commercial use only, Freeware but not in the public domain | SCR_014501 | Neuroscience Information Toolbox (NIT) | 2026-08-21 12:40:21 | 26 | |||||||||
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Complex Portal Resource Report Resource Website 1+ mentions |
Complex Portal (RRID:SCR_015038) | data or information resource, database, portal | Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download. | database, molecular complex, model organism | European Molecular Biology Laboratories Core Funding ; NIH 268201000035C; BBSRC BB/L024179/1 |
PMID:25313161 DOI:10.1093/nar/gku975 |
Open source, Available for download | r3d100013295 | https://doi.org/10.17616/R31NJMR3 | SCR_015038 | EBI Complex Portal | 2026-08-21 12:40:11 | 1 | ||||||
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CAWorks Resource Report Resource Website 1+ mentions |
CAWorks (RRID:SCR_014185) | data processing software, image analysis software, software application, software resource | A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. | image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement |
is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
NIMH 1R01 MH084803; NIBIB R01 EB008171; NIA 5U01AG033655; NCRR P41 RR015241; NIBIB R01 EB000975 |
Available to the research community | http://www.cis.jhu.edu/software/caworks/ | SCR_014185 | Computational Anatomy Works | 2026-08-21 12:40:17 | 2 | |||||||
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ASIPro Resource Report Resource Website 100+ mentions |
ASIPro (RRID:SCR_014547) | data processing software, image analysis software, software application, software resource | An image analysis software. | image analysis, image analysis software, image processing | SCR_014547 | ASIPro VM | 2026-08-21 12:40:23 | 127 | |||||||||||
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TissueQuest Analysis Software Resource Report Resource Website 10+ mentions |
TissueQuest Analysis Software (RRID:SCR_014822) | data processing software, image analysis software, software application, software resource | Image analysis software for cells and stained areas in samples stained with immunofluorescent markers. | image analysis software, stain, cell, immunofluorescence | is related to: HistoQuest Analysis Software | Commercially available | SCR_014822 | 2026-08-21 12:40:08 | 36 | ||||||||||
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Biorepositories and Biospecimens Research Branch Resource Report Resource Website 1+ mentions |
Biorepositories and Biospecimens Research Branch (RRID:SCR_013979) | data or information resource, portal | BBRB supports medical discovery and precision medicine by providing leadership, tools, and resources to the biobanking community. Provides input on policy related to biobanking and supports the availability of biospecimens for research. Develops standardized procedures for biospecimen science and research; conducts and sponsors research on the effects of biospecimen preanalytical factors; leads and supports major scientific initiatives requiring high-quality biospecimens; and supports investigations into the ethical, legal, and social issues concerning biospecimen collection and use. | portal, biospecimen, human biospecimen, cancer, cancer research, database, |
is listed by: Connected Researchers is related to: Biospecimen Research Database is related to: caHUB is related to: Connected Researchers has parent organization: National Cancer Institute |
cancer | Free, Freely available | http://biospecimens.cancer.gov/default.asp | SCR_013979 | , NCI’s Biorepositories and Biospecimen Research Branch (BBRB) | 2026-08-21 12:40:09 | 1 | |||||||
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OpenAIRE Resource Report Resource Website 10+ mentions |
OpenAIRE (RRID:SCR_013740) | data or information resource, portal, project portal | A research portal to share and obtain research data and journal articles openly accessible to all disciplines. Established to support the Open Access Policy, as set out by the ERC Scientific Council Guidelines for Open Access and the Open Access pilot launched by the European Commission. | open access, Europe, repository networks, project portal, research data, journal articles |
is related to: ZENODO is related to: Digital Repository Infrastructure Vision for European Research |
European Union | Free, Public | SCR_013740 | Open Access Infrastructure for Research in Europe | 2026-08-21 12:39:59 | 44 |
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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 U24DK097771.
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