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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Arkansas for Medical Sciences; Arkansas; USA Resource Report Resource Website 10+ mentions |
University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) | UAMS | data or information resource, organization portal, portal, department portal | Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care. | translational medicine, public medical school |
is related to: Alzheimers Disease Genetics Consortium is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Arkansas System; Arkansas; USA is parent organization of: UAMS Experimental Pathology Core Laboratory |
Free | grid.241054.6, nlx_152181, Wikidata:Q941298, Crossref funder ID:100008519, ISNI:0000 0004 4687 1637 | https://ror.org/00xcryt71 | SCR_002522 | University of Arkansas for Medical Sciences | 2026-08-10 09:31:45 | 41 | ||||||
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OpenDOAR Resource Report Resource Website 10+ mentions |
OpenDOAR (RRID:SCR_002641) | OpenDOAR | data or information resource, data repository, database, service resource, storage service resource | A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining. | open access, open data, repository, data sharing |
is listed by: FORCE11 is related to: DOAJ - Directory of Open Access Journals has parent organization: University of Nottingham; Nottingham; United Kingdom |
JISC | Free, Freely available | nlx_156070 | SCR_002641 | Directory of Open Access Repositories, The Directory of Open Access Repositories - OpenDOAR | 2026-08-10 09:31:47 | 40 | ||||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data or information resource, image repository, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | 2026-08-10 09:31:46 | 14 | |||||
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Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) Resource Report Resource Website 10+ mentions |
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) | PDBP | material storage repository, service resource, storage service resource, biospecimen repository | Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders. | parkinson's, clinical neuroinformatics, magnetic resonance, diagnostic, progression, biomarker, clinical |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NINDS Repository is related to: MIPAV: Medical Image Processing and Visualization has parent organization: National Institute of Neurological Disorders and Stroke |
Parkinson's disease | nlm ; NINDS |
PMID:25976927 | Restricted | nlx_155919 | http://www.nitrc.org/projects/pdbp | http://pdbp.ninds.nih.gov/index.jsp | SCR_002517 | Parkinson's Disease Biomarkers Program, PDBP: Parkinsons Disease Biomarkers Program, Parkinson’s Disease Biomarkers Program Data Management Resource, PDBP DMR | 2026-08-10 09:31:45 | 31 | ||
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TAPIR Resource Report Resource Website 50+ mentions |
TAPIR (RRID:SCR_002596) | TAPIR | software application, registration software, software resource, image analysis software, data processing software | A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_156001 | SCR_002596 | Tools for Advanced Parameterized Image Registration | 2026-08-10 09:31:46 | 67 | |||||||
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CKAN Resource Report Resource Website 10+ mentions |
CKAN (RRID:SCR_002622) | CKAN | software application, data management software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A complete out-of-the-box data management software solution that makes data accessible by providing tools to streamline publishing, sharing, finding and using data. CKAN is aimed at data publishers (national and regional governments, companies and organizations) wanting to make their data open and available. It uses its internal model to store metadata about the different records, and presents it on a web interface that allows users to browse and search this metadata. It also offers a powerful API that allows third-party applications and services to be built around it. CKAN is built with Python on the backend and Javascript on the frontend, and uses the Pylons web framework and SQLAlchemy as its ORM. Its database engine is PostgreSQL and its search is powered by SOLR. It has a modular architecture that allows extensions to be developed to provide additional features such as harvesting or data upload. CKAN is currently used by governments and user groups worldwide to power both official and community data portals. | data management, python, javascript |
is used by: Datahub is listed by: FORCE11 |
Free, Freely available | nlx_156038 | http://www.force11.org/node/4698 | SCR_002622 | ckan - The open source data portal software | 2026-08-10 09:31:46 | 19 | ||||||
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Stanley Neuropathology Consortium Integrative Database Resource Report Resource Website 10+ mentions |
Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) | SNCID | data or information resource, analysis service resource, production service resource, database, data set, service resource, data analysis service | A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access. | schizophrenia, bipolar disorder, depressive disorder, brain, blinded study, microarray, single-nucleotide polymorphism, mental disorder, biomarker | has parent organization: Stanley Medical Research Institute | Schizophrenia, Bipolar Disorder, Depressive Disorder, Mental disorder | PMID:19829293 | Free | nif-0000-24103 | SCR_002749 | Stanley Neuropathology Consortium Integrative Database | 2026-08-10 09:31:49 | 20 | |||||
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rsync Resource Report Resource Website 1+ mentions |
rsync (RRID:SCR_003113) | source code, software resource | Software that provides rapid incremental file transfer. | file transfer |
is used by: studyforrest.org has parent organization: Samba |
Free, Available for download, Freely available | nlx_156711 | SCR_003113 | 2026-08-09 09:03:41 | 7 | |||||||||
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Segtools Resource Report Resource Website 1+ mentions |
Segtools (RRID:SCR_004394) | source code, software resource | Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another. | has parent organization: University of Washington; Seattle; USA | PMID:22029426 | nlx_40271 | SCR_004394 | 2026-08-09 09:03:55 | 5 | ||||||||||
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University of Texas MD Anderson Cancer Center Resource Report Resource Website 500+ mentions |
University of Texas MD Anderson Cancer Center (RRID:SCR_004699) | MD Anderson Cancer Center | institution | The mission of The University of Texas MD Anderson Cancer Center is to eliminate cancer in Texas, the nation, and the world through outstanding programs that integrate patient care, research and prevention, and through education for undergraduate and graduate students, trainees, professionals, employees and the public. VISION: We shall be the premier cancer center in the world, based on the excellence of our people, our research-driven patient care and our science. We are Making Cancer History. |
is related to: National Chimpanzee Brain Resource has parent organization: University of Texas System; Texas; USA is parent organization of: MD Anderson Clone Bank is parent organization of: MD Anderson Pancreas Tissue Bank is parent organization of: MD Anderson Gynecologic Cancer Tissue Bank is parent organization of: VirusSeq is parent organization of: SpliceSeq is parent organization of: Chimpanzee Biomedical Research Resource is parent organization of: Owl Monkey Breeding and Research Resource is parent organization of: Squirrel Monkey Breeding and Research Resource is parent organization of: DupRecover is parent organization of: targetHub is parent organization of: Rhesus Monkey Breeding and Research is parent organization of: FamSeq is parent organization of: TAD is parent organization of: BreakFusion is parent organization of: RPPA Core Facility is parent organization of: University of Texas MD Anderson Cancer Center Advanced Microscopy Core Facility is parent organization of: University of Texas MD Anderson Functional Genomics Core Facility is parent organization of: University of Texas MD Anderson Research Histology Core Facility is parent organization of: University of Texas MD Anderson Cancer Center Small Animal Imaging Facility is parent organization of: A3D3a MVP is parent organization of: University of Texas MD Anderson Cancer Center Mass Spectrometry Imaging Core Facility |
Crossref funder ID: 100007313, nif-0000-24365, SCR_008276, nlx_69261, Wikidata: Q1525831, ISNI: 0000 0001 2291 4776, grid.240145.6 | https://ror.org/04twxam07 | SCR_004699 | UT M.D. Anderson Cancer Center, M.D. Anderson Cancer Center, UT MD Anderson Cancer Center | 2026-08-09 09:04:00 | 949 | ||||||||
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CPODES numerical integrator Resource Report Resource Website 1+ mentions |
CPODES numerical integrator (RRID:SCR_000766) | CPODES | source code, software resource | CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules. | dynamic, numerical integrator, multibody, source code |
uses: Simbody(tm): SimTK Multibody Dynamics Toolset is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23329 | SCR_000766 | 2026-08-09 09:03:02 | 6 | ||||||||
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BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | source code, software resource | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-08-09 09:03:51 | 21 | ||||||
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Laboratory of Neuro Imaging Resource Report Resource Website 50+ mentions |
Laboratory of Neuro Imaging (RRID:SCR_001922) | LONI | training resource, biomedical technology resource center | Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions. | anatomic, animal, brain, brain function, brain structure, cerebral metabolism, human, mapping, neurobiological, software, neuroimaging, fmri, mri, neuroimaging, software, brain mapping, computational software, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Wavelet Analysis of Image Registration is related to: Sub-Volume Thresholding Analysis is related to: jViewbox is related to: MultiPhase-SEG is related to: LONI Java Image I/O Plugins is related to: DualSurfaceMin is related to: Charged Fluid Model for Brain Image Segmentation is related to: MINC/Atlases has parent organization: University of Southern California Keck School of Medicine; California; USA is parent organization of: Center for Computational Biology at UCLA is parent organization of: LONI Visualization Tool is parent organization of: International Consortium for Brain Mapping is parent organization of: LONI Provenance Editor is parent organization of: TetraMetrix is parent organization of: Synchronized Histological Image Viewing Architecture is parent organization of: LONI ShapeViewer is parent organization of: LONI ShapeTools is parent organization of: FFT Library is parent organization of: Mouse BIRN Atlasing Toolkit is parent organization of: MGH-USC Human Connectome Project is parent organization of: Mouse Connectome Project is parent organization of: LONI Inspector is parent organization of: Parkinson's Progression Markers Initiative is parent organization of: BrainSolution is parent organization of: BrainGraph Editor is parent organization of: INVIZIAN is parent organization of: LONI Brain Parser is parent organization of: LONI De-identification Debablet is parent organization of: iTools is parent organization of: Pipeline Neuroimaging VirtualEnvironment is parent organization of: MultiTracer is parent organization of: International Consortium for Brain Mapping |
NCRR 5 P41 RR013642 | LONI Software License | nif-0000-10494 | http://www.nitrc.org/projects/loni | http://loni.ucla.edu/ | SCR_001922 | UCLA Laboratory of Neuro Imaging, Laboratory of Neuroimaging, UCLA LONI, USC Laboratory of Neuro Imaging | 2026-08-09 09:03:19 | 65 | ||||
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Genomedata Resource Report Resource Website 1+ mentions |
Genomedata (RRID:SCR_004544) | Genomedata | source code, software resource | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-08-09 09:03:55 | 1 | ||||||
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RNAplex Resource Report Resource Website 10+ mentions |
RNAplex (RRID:SCR_002763) | RNAplex | source code, software resource | Software tool to rapidly search for short interactions between two long RNAs. | interaction, rna, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Leipzig; Saxony; Germany |
PMID:21593134 PMID:18434344 |
Free, Freely available, Available for download | rid_000107, biotools:rnaplex | https://bio.tools/rnaplex | SCR_002763 | 2026-08-09 09:03:35 | 37 | ||||||
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Time-resolved and time-scale adaptive measures of spike train synchrony Resource Report Resource Website 1+ mentions |
Time-resolved and time-scale adaptive measures of spike train synchrony (RRID:SCR_001667) | Time-resolved and time-scale adaptive measures of spike train synchrony | source code, software resource | Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616 | synchrony, spike train, time series analysis, synchronization, clustering, neuronal coding | has parent organization: Pompeu Fabra University; Barcelona; Spain | Marie Curie Individual Outgoing Fellowship ; Spanish Ministry of Education and Science BFU2007-61710; European Social Fund 2008FI-B 00460 |
PMID:21129402 PMID:19591867 |
Free, Freely Available | nlx_153991 | SCR_001667 | 2026-08-09 09:03:14 | 1 | ||||||
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Visual Molecular Dynamics Resource Report Resource Website 100+ mentions |
Visual Molecular Dynamics (RRID:SCR_001820) | VMD | source code, software resource | A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | standalone software, mac os x, unix, virtual machine, windows, c++ |
is listed by: OMICtools has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS | PMID:8744570 | Free, Freely available | OMICS_03804 | SCR_001820 | 2026-08-09 09:03:17 | 383 | ||||||
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Reliable detection of directional couplings using rank statistics Resource Report Resource Website 1+ mentions |
Reliable detection of directional couplings using rank statistics (RRID:SCR_001662) | Reliable detection of directional couplings using rank statistics | source code, software resource | Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217. | directional coupling, time series, rank statistics, normalization, experimental signal | has parent organization: Pompeu Fabra University; Barcelona; Spain | PMID:19792241 | Free, Freely Available | nlx_153987 | SCR_001662 | 2026-08-09 09:03:18 | 1 | |||||||
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XP-CLR Resource Report Resource Website 50+ mentions |
XP-CLR (RRID:SCR_004961) | source code, software resource | XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available. | has parent organization: Harvard Medical School; Massachusetts; USA | Restricted | nlx_94751 | https://reich.hms.harvard.edu/software | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004961 | XP-CLR Software | 2026-08-09 09:04:04 | 74 | |||||||
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ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | source code, software resource | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-08-09 09:04:10 | 5 |
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