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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PTNet Resource Report Resource Website |
PTNet (RRID:SCR_022975) | software resource, source code | Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression. | protein level, protein expression estimation, miRNA-mRNA interactions, mRNA expression, miRNA expression, | NIDDK DK097771; NIGMS R01GM113952; NSF III1755761 |
DOI:10.1093/bib/bbab264 | Free, Available for download, Freely available | SCR_022975 | 2026-09-03 05:08:16 | 0 | |||||||||
|
abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | software resource, source code | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Harvard University ; Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596 |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-09-03 05:09:27 | 1 | ||||||||
|
BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | software resource, source code | Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs. | OpenBehavior, automated behavioral detection, markerless pose tracking, detect frame by frame behavior, video time series, kinematic and postural statistics, |
is listed by: OpenBehavior is related to: SLEAP, LEAP and MotionMapper project works with: DeepLabCut |
Brain and Behavior Research Foundation ; Brain Research Foundation ; NIMH K01MH116264; NIMH K08MH116125; NIMH T32MH073526; NSF ; Simonsen Foundation ; Whitehall Foundation |
PMID:35997072 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/behaviordepot/ | SCR_023602 | 2026-09-03 05:09:33 | 2 | |||||||
|
PhysiCell Studio Resource Report Resource Website 10+ mentions |
PhysiCell Studio (RRID:SCR_025311) | software resource, source code | Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell. | create, execute, visualize, multicellular model, create initial positions of cells, | Breast Cancer Research Foundation ; European Commission ; Jayne Koskinas Ted Giovanis Foundation for Health and Policy ; NCI U01 CA232137; NSF |
PMID:37961612 | Free, Available for download, Freely available | SCR_025311 | 2026-09-03 05:09:51 | 15 | |||||||||
|
lcMLkin Resource Report Resource Website 1+ mentions |
lcMLkin (RRID:SCR_025418) | software resource, source code | C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data. | C++, Maximum Likelihood Estimation, Biological Relatedness, Low Coverage Sequencing Data, | NSF | DOI:10.1101/023374 | Free, Available for download, Freely available | SCR_025418 | Maximum Likelihood Estimation of Relatedness | 2026-09-03 05:09:25 | 5 | ||||||||
|
MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | data analysis software, data processing software, software application, software resource | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | Gillings Innovation Laboratory in Statistical Genomics ; NCI R01 CA138255; NIEHS R01 ES015241; NIMH R01 MH090936; NSF ; US Environmental Protection Agency |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-09-03 05:10:05 | 75 | ||||||||
|
ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | software resource, source code | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; National Research Foundation of Korea ; NIAID R21AI156595; NIH Office of the Director DP5OD026389; NSF ; Seoul National University ; University of Göttingen |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | 2026-09-03 05:09:50 | 493 | ||||||||
|
MorphoSource Resource Report Resource Website 100+ mentions |
MorphoSource (RRID:SCR_025654) | data or information resource, database | Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage. | 3D media, 2D media, physical objects, natural history, cultural heritage, scientific collections, shared cultural heritage, | Duke University ; NSF |
Free, Freely available, | r3d100012224 | https://github.com/MorphoSource, https://doi.org/10.17616/R35Q0K | SCR_025654 | 2026-09-03 05:09:35 | 104 | ||||||||
|
SomaticSignatures Resource Report Resource Website 1+ mentions |
SomaticSignatures (RRID:SCR_025620) | software resource, software toolkit, source code | Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. | R, identifying mutational signatures, single nucleotide variants, high-throughput experiments, | NSF | PMID:26163694 | Free, Available for download, Freely available, | https://github.com/juliangehring/SomaticSignatures | SCR_025620 | 2026-09-03 05:09:59 | 7 | ||||||||
|
ezBIDS Resource Report Resource Website 1+ mentions |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | BRAIN CONNECTS ; Kavli Foundation ; NIBIB R01EB029272; NIBIB R01EB030896; NIMH R01MH133701; NINDS UM1NS132207; NSF ; Spanish Government ; Wellcome Trust |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-09-03 05:09:59 | 1 | |||||||
|
Efficient Permutation Testing Resource Report Resource Website |
Efficient Permutation Testing (RRID:SCR_014104) | software resource, source code | A Matlab implementation for efficient permutation testing by using matrix completion. | permutation, nueroimaging, source code, fast, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Wisconsin Partnership Fund ; NIA R01 AG040396; NSF CAREER 1252725; NSF RI 1116584; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; Veterans Administration Merit Review I01CX000165 |
Available for download, Acknowledgement requested | http://pages.cs.wisc.edu/~vamsi/pt_fast.html | SCR_014104 | Speeding Up Permutation Testing in Neuroimaging | 2026-09-03 05:07:52 | 0 | |||||||
|
SpikeHunter Resource Report Resource Website 1+ mentions |
SpikeHunter (RRID:SCR_024831) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins. | identifying phage tailspike proteins, phage tailspike protein, deplolymerase, right-handed beta-helix, | NLM ; NSF |
PMID:37503040 | Free, Available for download, Freely available | SCR_024831 | 2026-09-03 05:09:06 | 1 | |||||||||
|
Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NHGRI R01 HG011883; NHGRI R01HG010773; NIGMS R01 GM126553; NIMH R01MH110531; NIMH R01MH116281; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-09-03 05:09:12 | 1 | ||||||||
|
PyContact Resource Report Resource Website 1+ mentions |
PyContact (RRID:SCR_025066) | data analysis software, data processing software, software application, software resource | Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package. | non-covalent interactions, molecular dynamics trajectories, | is related to: MDAnalysis | German Research Foundation ; NIGMS P41 GM104601; NSF |
PMID:29414703 | Free, Available for download, Freely available, | https://github.com/maxscheurer/pycontact | SCR_025066 | 2026-09-03 05:09:18 | 3 | |||||||
|
Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | atlas, data or information resource, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | BBSRC ; Carnegie Trust for the Universities of Scotland ; Ministry of Science ; Technology and Telecommunications of Costa Rica ; Natural Sciences and Engineering Research Council of Canada ; NCCIH AT008718; NCCIH F31 AT010098; NCCIH T32 AT007533; NCCIH U41 AT008718; NCI F31 CA236237; Netherlands eScience Center ; NIGMS GM124461; NIGMS R01 GM125943; NIH D43 TW010530; NSERC Discovery ; NSF ; Sao Paulo Research Foundation |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-09-03 05:09:50 | 36 | ||||||
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National High Magnetic Field Laboratory High B/T Core Facility Resource Report Resource Website |
National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) | B/T | access service resource, core facility, service resource | Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory. | Magnetic, field, temperature | is related to: University of Florida; Florida; USA | Department of Defense ; Department of Energy ; Florida State ; NIH ; NSF DMR-1644779 |
Restricted | SCR_017360 | NHMF Laboratory High B/T Facility, High B/T (magnetic field / temperature) Facility, High B/T Facility | 2026-09-03 05:08:18 | 0 | |||||||
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National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility Resource Report Resource Website 500+ mentions |
National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility (RRID:SCR_017362) | AMRIS | access service resource, core facility, service resource | National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development. | Nuclear Magnetic Resonance, Magnetic Resonance Imaging, spectroscopy, magnetic resonans, scanner, magnet |
has parent organization: National High Magnetic Field Laboratory has parent organization: University of Florida; Florida; USA |
Department of Defense ; Department of Energy ; NSF DMR-1157490; NSF DMR-1644779; NSF DMR-2128556; State of Florida |
Restricted | SCR_017363 | https://nationalmaglab.org/user-facilities/nmr-mri, https://nationalmaglab.org | SCR_017362 | , Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Facility | 2026-09-03 05:08:23 | 859 | |||||
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University of Delaware BioImaging Center Core Facility Resource Report Resource Website 1+ mentions |
University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) | access service resource, core facility, service resource | Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies. | Microscopy, bioimaging, confocal, electron, microscope, analysis, service, core |
is listed by: ABRF CoreMarketplace has parent organization: University of Delaware; Delaware; USA |
NCRR S10 RR027273; NIGMS P20 GM103446; NIGMS P20 GM113125; NIH Office of the Director S10 OD016361; NIH Office of the Director S10 OD025165; NSF IIA 1301765; State of Delaware |
Open | ABRF_537 | https://coremarketplace.org/?FacilityID=537&citation=1 | SCR_017814 | Delaware University BioImaging Center Core Facility, University of Delaware Bio-Imaging Center | 2026-09-03 05:08:01 | 1 | ||||||
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Delaware University Surface Analysis Core Facility Resource Report Resource Website |
Delaware University Surface Analysis Core Facility (RRID:SCR_017796) | access service resource, core facility, service resource | Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM). | Surface, analysis, X-ray, photoelectron, spectroscopy, ion, mass, spectrometry, imaging, Auger, microscopy, scattering, scanning, probe, service, core | NSF | Open | ABRF_439 | SCR_017796 | Surface Analysis Facility | 2026-09-03 05:08:00 | 0 | ||||||||
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Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility (RRID:SCR_017877) | CLaMMP | access service resource, core facility, service resource | Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials. | Material, mechanical, property, testing, solid, service, core, ABRF | is listed by: ABRF CoreMarketplace | NSF DMR 1720139 | Open | ABRF_727 | SCR_017877 | Central Laboratory for Materials Mechanical Properties | 2026-09-03 05:07:43 | 3 |
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