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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Rfam Resource Report Resource Website 1000+ mentions |
Rfam (RRID:SCR_007891) | Rfam, RFAM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome | family, genome, clan, structure, non-coding rna, FASEB list | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | Howard Hughes Medical Institute ; University of Manchester; Manchester; United Kingdom ; Wellcome Trust WT077044/Z/05/Z |
PMID:21062808 | http://rfam.sanger.ac.uk/ | SCR_007891 | RFAM, Rfam database | 2026-09-12 12:56:57 | 4040 | ||||||
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University of Rennes 1; Rennes; France Resource Report Resource Website 1+ mentions |
University of Rennes 1; Rennes; France (RRID:SCR_007649) | Univ-Rennes 1 | university | The University of Rennes 1 is one of the two main universities in the city of Rennes, France. It is under the Academy of Rennes. It specializes in science, technology, law, economy, management and philosophy. |
is related to: MIP-DILI is related to: Empenn is parent organization of: VISAGES Research is parent organization of: GASSST is parent organization of: CoBaltDB |
nlx_31280 | SCR_007649 | Universite de Rennes 1, University of Rennes 1, Université de Rennes 1 | 2026-09-12 12:56:57 | 1 | |||||||||
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BRIG Resource Report Resource Website 500+ mentions |
BRIG (RRID:SCR_007802) | BRIG | software resource | A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1186/1471-2164-12-402 | OMICS_00929, biotools:brig | https://bio.tools/brig, https://sources.debian.org/src/brig/ | SCR_007802 | BLAST Ring Image Generator | 2026-09-12 12:56:57 | 561 | ||||||
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ERIC Resource Report Resource Website 500+ mentions |
ERIC (RRID:SCR_007644) | ERIC | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | ERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | enterobacteria, enterobacteria pathogen, biodefense, disease bioinformatics, human disease, pathogen, pathogenic bacteria, cronobacter, enterobacter, erwinia, klebsiella, pectobacterium, photorhabdus, proteus, serratia, escherichia, shigella, salmonella, yersinia, citrobacter, FASEB list | has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02813 | http://www.ericbrc.org | SCR_007644 | Enteropathogen Resource Integration Center (ERIC), Enteropathogen Resource Integration Center | 2026-09-12 12:56:57 | 950 | |||||
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SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, data processing software, software application, software resource | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Health ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-09-12 12:57:14 | 31 | ||||||
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U.S. Department of Commerce Resource Report Resource Website 1+ mentions |
U.S. Department of Commerce (RRID:SCR_009859) | Commerce.gov | institution | Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards. | Government granting agency |
is parent organization of: NIST - National Institute of Standards and Technology is parent organization of: National Oceanic and Atmospheric Administration is parent organization of: U.S. Census Bureau |
Crossref funder ID: 100000190, grid.239119.1, ISNI: 0000 0004 0478 6426, Wikidata: Q503577, nlx_144074 | https://ror.org/04chq2495 | SCR_009859 | United States Department of Commerce | 2026-09-12 12:57:15 | 2 | |||||||
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Fiber Optic Button Response System Resource Report Resource Website 10+ mentions |
Fiber Optic Button Response System (RRID:SCR_009577) | instrument resource | Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed. | eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, response monitoring, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | https://drive.google.com/file/d/1vvm02GkPgAG6LnRzWE9FEQZD6JSqtngA/view?usp=drivesdk | nlx_155759 | http://www.nitrc.org/projects/fobrs, https://pstnet.com/wp-content/uploads/2021/04/Celeritas-Operator-Manual.pdf | SCR_009577 | Celeritas Fiber Optic Response System | 2026-09-12 12:57:13 | 22 | |||||||
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Oregon State University; Oregon; USA Resource Report Resource Website 1+ mentions |
Oregon State University; Oregon; USA (RRID:SCR_009731) | university | Public research university in Corvallis, Oregon. The university currently offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. |
is parent organization of: TileQC is parent organization of: AFTOL is parent organization of: CASHX is parent organization of: Chromaseq is parent organization of: Plant Ontology is parent organization of: Plant Ontology is parent organization of: Northern Spalting - Applied Mycology Lab is parent organization of: EnVision Manager is parent organization of: Oregon State University Center for Quantitative Life Sciences Core Facility is parent organization of: Oregon State University Electron Microscopy Core Facility has organization facet: pathogensurveillance |
Wikidata:Q861888, ISNI:0000 0001 2112 1969, Crossref funder ID:100009612, nlx_87751, grid.4391.f | https://ror.org/00ysfqy60 | SCR_009731 | 2026-09-12 12:57:15 | 2 | ||||||||||
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MazeSuite Resource Report Resource Website 10+ mentions |
MazeSuite (RRID:SCR_009606) | MazeSuite | data processing software, data visualization software, software application, software resource, software toolkit | A complete set of tools that enables researchers to perform spatial and navigational behavior experiments within interactive, easy to create, and extendable (e.g., multiple rooms) 3D virtual environments. MazeSuite can be used to design/edit adapted 3D environments where subjects? behavioral performance can be tracked. Maze Suite consists of three main applications; an editing program to create and alter maps (MazeMaker), a visualization/rendering module (MazeWalker), and finally an analysis/mapping tool (MazeAnalyzer). Additionally, MazeSuite has the capabilities of sending signal pulses to physiological recording devices using standard computer ports. MazeSuite, with all 3 applications, is a unique and complete toolset for researchers who want to easily and rapidly deploy interactive 3D environments. Requirements Maze Suite is designed for Windows 7, Windows Vista and Windows XP. 3D rendering quality depends on available graphics card hardware; OpenGL 2.1 or above compliant is recommended. For Windows XP systems, .NET Framework Version 2.0 or above is required and can be downloaded from Microsoft's website. | eeg, meg, electrocorticography, optical imaging, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Drexel University; Pennsylvania; USA |
PMID:18411560 | Account required, Non-commercial, Software License Agreement, Http://mazesuite.com/forum/ucp.php?mode=terms&sid=7373a682447f060f67ec8693b7e470f7 | nlx_155807 | http://www.nitrc.org/projects/mazesuite | SCR_009606 | Maze Suite | 2026-09-12 12:57:14 | 12 | |||||
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Mango Resource Report Resource Website 100+ mentions |
Mango (RRID:SCR_009603) | Mango | data processing software, data visualization software, image analysis software, image processing software, software application, software resource | A viewer for medical research images that provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform: * Mango ? Desktop ? Mac OS X, Windows, and Linux * webMango ? Browser ? Safari, Firefox, Chrome, and Internet Explorer * iMango ? Mobile ? Apple iPad Key Features: * Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats * Customizable: Create plugins, custom filters, color tables, file formats, and atlases * ROI Editing: Threshold and component-based tools for painting and tracing ROIs * Surface Rendering: Interactive surface models supporting cut planes and overlays * Image Registration: Semi-automatic image coregistration and manual transform editing * Image Stacking: Threshold and transparency-based image overlay stacking * Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics * Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators | analyze, atlas application, console (text based), dicom, gifti, java, linux, macos, microsoft, magnetic resonance, nifti, os independent, platform, posix/unix-like, quantification, region of interest, registration, rendering, segmentation, spatial transformation, statistical operation, sunos/solaris, surface analysis, temporal transformation, visualization, volumetric analysis, web environment, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
NIBIB P01-EB01955; NIBIB R01-EB015314-01a1; NIMH R01-MH074457 |
Free | nlx_155804 | http://www.nitrc.org/projects/mango | SCR_009603 | Multi-image Analysis GUI | 2026-09-12 12:57:14 | 491 | |||||
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EEGVIS Resource Report Resource Website 1+ mentions |
EEGVIS (RRID:SCR_009569) | EEGVIS | data processing software, data visualization software, software application, software resource, software toolkit | A MATLAB toolbox for exploration of multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. The toolbox can be used directly in MATLAB at any stage in a user's processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license. The toolbox also supplies a number of extensible base classes for users who wish to develop their own visualizations. | reusable library, eeg, meg, electrocorticography, matlab, statistical operation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:22654753 | GNU General Public License | nlx_155749 | http://www.nitrc.org/projects/eegvis | SCR_009569 | 2026-09-12 12:57:13 | 1 | ||||||
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ISRNA Resource Report Resource Website 1+ mentions |
ISRNA (RRID:SCR_009565) | ISRNA | software resource | An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:24300438 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00360 | SCR_009565 | Integrative Short Reads NAvigator | 2026-09-12 12:57:13 | 3 | |||||||
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Pipeline System for Octave and Matlab Resource Report Resource Website 1+ mentions |
Pipeline System for Octave and Matlab (RRID:SCR_009637) | PSOM | data processing software, software application, software library, software resource, software toolkit, workflow software | A lightweight software library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab / Octave structure. PSOM then automatically offers the following services: * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures : successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess ! | reusable library, linux, macos, matlab, microsoft, posix/unix-like, windows, workflow, octave, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Montreal; Quebec; Canada |
PMID:22493575 | MIT License | nlx_155924 | http://www.nitrc.org/projects/psom | SCR_009637 | 2026-09-12 12:57:14 | 3 | ||||||
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NordicNeuroLab Resource Report Resource Website 50+ mentions |
NordicNeuroLab (RRID:SCR_009632) | NNL | commercial organization | From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike. | analyze, ascii, dicom, diffusion mr fiber tracking, experiment control, eye tracking, fiber tracking, haemodynamic response, hardware, microsoft, magnetic resonance, nifti, perfusion, physiological recording, scanner, stimulus presentation, temporal curve fitting, temporal transformation, tractography, windows, windows vista, windows xp, fmri, post-processing, visualization, bold, diffusion, dti, perfusion, dce, audio stimulation, visual stimulation, eye tracking, patient response, clinical, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial | nlx_155905 | http://www.nitrc.org/projects/nnl | SCR_009632 | 2026-09-12 12:57:14 | 57 | |||||||
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PICSL Multi-Atlas Segmentation Tool Resource Report Resource Website 1+ mentions |
PICSL Multi-Atlas Segmentation Tool (RRID:SCR_009633) | PICSL Multi-Atlas Segmentation Tool | data processing software, image analysis software, segmentation software, software application, software resource | This package contains a software implementation for joint label fusion and corrective learning, which were applied in MICCAI 2012 Grand Challenge on Multi-Atlas Labeling and finished in the first place. Joint label fusion is for combining candidate segmentations produced by registering and warping multiple atlases for a target image. Corrective learning can be applied to further reduce systematic errors produced by joint label fusion. In general, corrective learning can be applied to correct systematic errors produced by other segmentation methods as well. | atlas application, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155914 | SCR_009633 | 2026-09-12 12:57:14 | 2 | ||||||||
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NIRS-SPM Resource Report Resource Website 100+ mentions |
NIRS-SPM (RRID:SCR_009630) | NIRS-SPM | data analysis software, data processing software, software application, software resource | A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | optical imaging, near-infrared spectroscopy, spm, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Korea Advanced Institute of Science and Technology; Daejeon; South Korea |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155885 | http://www.nitrc.org/projects/nirs_spm | SCR_009630 | 2026-09-12 12:57:14 | 137 | |||||||
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Lipsia Resource Report Resource Website 10+ mentions |
Lipsia (RRID:SCR_009595) | Lipsia | data processing software, image analysis software, image processing software, software application, software resource | Software tool for processing functional magnetic resonance imaging (fMRI) data.Software system for evaluation of functional magnetic resonance images of human brain. | magnetic resonance, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany |
PMID:11679206 | Free, Available for download, Freely available | nlx_155787 | http://www.nitrc.org/projects/lipsia, https://sources.debian.org/src/lipsia/ | SCR_009595 | Lipsia: Leipzig Image Processing and Statistical Inference Algorithms ? a tool for fMRI data analysis, Leipzig Image Processing and Statistical Inference Algorithms, Lipsia: Leipzig Image Processing and Statistical Inference Algorithms | 2026-09-12 12:57:14 | 41 | |||||
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LIMO EEG Resource Report Resource Website 10+ mentions |
LIMO EEG (RRID:SCR_009592) | LIMO EEG | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A matlab toolbox (EEGlab compatible) allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with the tool. Across subject analyses are performed using bootstrap offering robust inferences. | reusable library, application, eeg, meg, electrocorticography, matlab, os independent, time domain analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155782 | http://www.nitrc.org/projects/limo_eeg | SCR_009592 | 2026-09-12 12:57:14 | 11 | |||||||
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MASIMatlab Resource Report Resource Website 1+ mentions |
MASIMatlab (RRID:SCR_009506) | MASIMatlab | software resource | This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling. | magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
nlx_155655 | SCR_009506 | 2026-09-12 12:57:13 | 4 | |||||||||
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iView X MRI-LR - Eye Tracking for fMRI Resource Report Resource Website 1+ mentions |
iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) | iView X MRI-LR | software resource | A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output | magnetic resonance, fmri, meg, eye, eye tracking, mri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commerical | nlx_155853 | http://www.nitrc.org/projects/iviewx_mri-lr | SCR_009627 | 2026-09-12 12:57:14 | 3 |
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