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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Autopatcher Resource Report Resource Website 1+ mentions |
Autopatcher (RRID:SCR_017464) | software application, software resource | Software tool for neuronal recording in intact brain. | Neuronal, recording, intact, brain, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH106027 | PMID:29297466 | Free, Available for download, Freely available | SCR_017464 | 2026-08-15 11:29:58 | 2 | ||||||||
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Fastqtl Resource Report Resource Website 100+ mentions |
Fastqtl (RRID:SCR_016093) | Fastqtl | software toolkit, software resource | Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq. | molecular, phenotype, multiply, testing, genotype, correct, genomic dataset, trait, loci, cis, quantitative, multi dimensional |
is listed by: Debian is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
European Commission SYSCOL FP7; European Research Council ; Louis Jeantet Foundation ; Swiss National Science Foundation ; SystemsX ; NIH-NIMH (GTEx) ; Helse Sør Øst |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-08-15 11:29:55 | 133 | ||||
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GPS Resource Report Resource Website 50+ mentions |
GPS (RRID:SCR_016374) | GPS | algorithm resource, software resource | Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode. | phosphorylate, protein, seq, predictive, substrate, site, kinase, mass spectrometry | PMID:18463090 | Free for academic use, Request for commercial use, Available for download | SCR_016374 | Group-based Prediction System, GPS: Group-based Prediction System, Group-based Prediction System (GPS) | 2026-08-15 11:30:05 | 69 | ||||||||
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Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software toolkit, software resource | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-08-15 11:29:56 | 4 | ||||||
|
Bootstrap CSS Resource Report Resource Website 10+ mentions |
Bootstrap CSS (RRID:SCR_016096) | programming language, software resource | Programming language framework for HTML, CSS, and JS. It is used for developing responsive, mobile projects on the web. | coding, framework, programming, development, mobile, project, web, application, html, css, js | Open source, Available for download | https://github.com/twbs/bootstrap | SCR_016096 | Bootstraps | 2026-08-15 11:30:03 | 11 | |||||||||
|
Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | software application, standalone software, software resource | Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. | Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom |
is listed by: Debian is listed by: OMICtools works with: Artemis: Genome Browser and Annotation Tool |
Wellcome Trust | PMID:16837528 DOI:10.1093/bioinformatics/btl369 |
Free, Available for download | OMICS_08280 | https://sources.debian.org/src/alien-hunter/, https://sources.debian.org/src/alien-hunter/ | SCR_015967 | 2026-08-15 11:30:02 | 6 | ||||||
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OpenBehavior Resource Report Resource Website 1+ mentions |
OpenBehavior (RRID:SCR_015938) | OB | software repository, software resource | Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects. | software, data, hardware, animal, behavior, cognition, cognitive, analysis, processing |
lists: Feeding Experimentation Device project lists: Bpod lists: SLEAP, LEAP and MotionMapper project lists: Social LEAP lists: MotionMapper lists: Behavioral Segmentation of Open-field in DeepLabCut project lists: DeepBehavior project lists: BonZeb project lists: D-Track project lists: Online Animal Tracker project lists: Locomouse project lists: openEyeTrack project lists: DeepPoseKit project lists: DeepFly3D project lists: neurotic project lists: Rodent Arena Tracker project lists: Open Source Whisking Video Database portal lists: Simple Behavior Analysis project lists: OpenMonkeyStudio project lists: FaceSync project lists: Online Animal Tracker lists: DeepBehavior lists: BonZeb lists: Behavioral Segmentation of Open-field in DeepLabCut lists: FaceSync lists: LocoMouse lists: DeepPoseKit lists: openEyeTrack lists: D-Track lists: Simple Behavior Analysis lists: DeepFly3D lists: Open Source Whisking Video Database lists: neurotic lists: Low Cost Open Source Eye Tracking project lists: Stytra project lists: Calcium ActiVity Explorer project lists: idtracker.ai project lists: Live Mouse Tracker project lists: ToxTrac project lists: Picamera project lists: EthoScopes project lists: Worm Behavior Platform project lists: KineMouse Wheel project lists: Mousecam project lists: M-Track project lists: ezTrack project lists: FaceMap project lists: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project lists: ZebraTrack project lists: LocoWhisk project lists: EthoWatcher project lists: Skinner Box project lists: Behavioral Observation Research Interactive Software project lists: Pyper project lists: Automated Rodent Tracker project lists: LinCoM project lists: Bonsai project lists: Quantifying Animal Movement from Pre-recorded Videos project lists: Platform for Acoustic STArtle project lists: Joystick project lists: 3DTracker project lists: AutoPilot project lists: PiDose project lists: DeepSqueak project lists: Rigbox project lists: Catalepsy Bar project lists: Dual port Lick Detector project lists: Pathfinder project lists: Actifield project lists: Rodent Activity Detector project lists: flyPAD project lists: Automated Home Cage Rodent Two bottle Choice Test project lists: MedParse project lists: Voluntary Access Static Incapacitance Chamber project lists: Laubach Lab GitHub Repository project lists: BPM Biosignals project lists: Automated mouse homecage two bottle choice test project lists: Mousetrap project lists: Autoreward2 project lists: Optimouse project lists: Hao Chen Lab Repository project lists: AutonoMouse project lists: Spike Forest project lists: Closed Loop System project lists: ArduiPod Box project lists: Oculomatic Eye Tracking project lists: Ultrasonic Vocalizations Detector project lists: Attys project lists: Calcium Imaging data Analysis project lists: Feldman Lab Lickometer project lists: MNE Scan project lists: Open Source platform for Sensory Tasks project lists: Scintillate project lists: Pypreclin project lists: Wave Surfer project lists: An open source motorized swivel for in vivo neural and behavioral recordings project lists: Toolboxes for Spike and LFP Analysis project lists: BrainGlobe project lists: UCLA Miniscope project lists: Cerebro Wireless Optogenetic System project lists: Home Cage Automated Skilled Reaching Apparatus project lists: Open-tES project lists: Capactive Touch Sensor project lists: CapTouch project lists: Two Armed Bandit Task project lists: Novel Gustometer for Human Taste Research project lists: OpenVape project lists: Calcium ActiVity Explorer lists: Pi Virtual Reality System project lists: BonVision project lists: FinchScope project lists: Mousecam lists: ezTrack lists: DIY-NAMIC project lists: Precision Syringe Pump Controller project lists: idtracker.ai lists: Stytra lists: EthoScopes lists: Worm Behavior Platform lists: Ardbark project lists: FaceMap lists: M-Track lists: ToxTrac lists: Pyper lists: Low Cost Open Source Eye Tracking lists: Automated Rodent Tracker lists: Live Mouse Tracker analysis lists: LinCoM lists: Skinner Box lists: 3DTracker lists: Pathfinder lists: Behavioral Observation Research Interactive Software lists: MNE Scan lists: Quantifying Animal Movement from Pre-recorded Videos lists: Rigbox lists: Platform for Acoustic STArtle lists: DeepSqueak lists: Oculomatic lists: Wave Surfer lists: EthoWatcher lists: MedParse lists: Bonsai lists: Scintillate lists: AutoPilot lists: Spike Forest lists: flyPAD lists: Optimouse lists: Calcium Imaging data Analysis lists: BonVision lists: Dual Port Lick Detector lists: Pypreclin lists: ACRoBaT lists: Visual stimulator with customizable light spectra lists: ToneBox lists: 3DOC lists: MouseBytes lists: Touchscreen Cognition lists: FreemoVR project lists: Modular Automated Platform for Large Scale Experiments project lists: OpenFeeder lists: SnackClock lists: SignalBuddy lists: ArControl project lists: Airtrack lists: Teensy-Based Interface project lists: Autonomous Training of a Forelimb Motor Task project lists: Ratcave project lists: DIY Rodent Running Disk lists: Moving Wall Box lists: Operant Box for Auditory Tasks project lists: Camera Control project lists: FlyPi lists: CerebraLux lists: Automated Home-Cage Functional Imaging project lists: Pearce Lab Syringe Pump project lists: Craniobot project lists: PhotometryBox lists: Pulse Pal project lists: NINscope lists: Nose Poke Device lists: pyControl project lists: OpenMV project lists: Rodent Operant Bucket project lists: Tetroplater lists: OpenSpritzer lists: Argus lists: NeRD lists: PRiED lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project lists: MouseMove project lists: Eco-HAB lists: Homecage Task Training and Mesoscale Imaging project lists: Microwave based Homecage Motion Detector project lists: CHEndoscope lists: Robotic Flower System for Bee Behavior project lists: TRIO Platform lists: A Head Mounted Multi Camera System for Freely Moving Mice project lists: Ratcave lists: 4 Port Nose Poke lists: An Opensource lickometer and microstructure analysis program lists: Automated Classification of Self-grooming in Mice project lists: FreemoVR lists: ArControl lists: Visual Discrimination with an iPad lists: Teensy-Based Interface lists: Operant Box for Auditory Tasks lists: Autonomous Training of a Forelimb Motor Task lists: 3D Printed Headcap and Microdrive lists: poke device arduino lists: MouseBytes lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology lists: Rodent Operant Bucket lists: Camera Control lists: linear actuator lists: Modular Automated Platform for Large Scale Experiments lists: pyControl lists: Argus lists: NINscope software lists: OpenMV lists: MouseMove lists: chendoscope lists: craniobot lists: Pulse Pal lists: Automated Home-Cage Functional Imaging lists: AutoHeadFix lists: SpikeGadgets lists: Open Ephys lists: MRI-stereoscope project lists: AutomaticSleepScoringTool lists: Pi-based Remote Acquisition Technology for Motion Capture project lists: Pi-based Remote Acquisition Technology for Motion Capture lists: Brainrender lists: TetrODrive lists: COMPASS lists: Cellpose lists: OORTT lists: DBscorer lists: GazeMetrics lists: AutoStereota lists: FlyBrainLab lists: pyOS-5 project lists: Pyneal lists: pyOS-5 lists: Atlas Based Analysis lists: VocalMat lists: DABEST lists: Raspberry Pi based auditory stimulus generator lists: Pain Assessment at Withdrawal Speeds lists: Florida research open source synchronization tool lists: Permuco lists: LED Matrix Stimuli lists: Mouse Action Recognition System lists: Behavior Ensemble and Neural Trajectory Observatory lists: Neonatal Stereotaxic Mouse Adaptor lists: MARS Developer lists: EZcalcium lists: MRI Compatible Microdrive lists: GuPPy lists: DeepEthogram lists: Pycro Manager lists: DeepBhvTracking lists: TweetyNet lists: OpenPose lists: TRex lists: SIPEC lists: Closed Loop Automated Reaching Apparatus lists: Timed pressure control hardware and software for delivery of air mediated distensions in animal models lists: CellExplorer lists: DLStream lists: SipperViz lists: Variational Embedding of Animal Motion lists: SHARCQ lists: PavCA project lists: GoFish Ajuwon etal 2022 lists: LED Zappelin’ lists: Minian lists: Modular LED Displays project lists: OpenSync lists: USVCAM lists: Histological E data Registration in rodent Brain Spaces lists: Pi USB Cam project lists: 3D Printed Superfusion Chamber lists: pyPhotometry lists: Rtrack lists: ColonyTrack lists: Anipose lists: LiftPose3D lists: DANNCE lists: DeepLabCut Project lists: ACTman lists: Raspberry Pi Grating lists: Falcon lists: OpBox lists: Mouse Behavioral Analysis Toolbox lists: Pynapple lists: Wheel Running Activity acQuisition lists: CaT-z lists: M3 Platform lists: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory lists: Rasberry rat lists: RodentJoystick lists: tmilltracker lists: 3D Printed Multi Pump System lists: BehaviorDEPOT lists: Open Face Homecage Running Wheel lists: RatHeadphones lists: RatInABox lists: LabNet lists: JAX Animal Behavior System lists: AnimalTA lists: Mousebytes lists: Lick Instance Quantifier Home cage Device lists: B-CALM lists: Freibox lists: commutator lists: Customized Guide Cannulas lists: BrainWAVE lists: Brainways lists: LFP Monitoring lists: PyMouseTracks lists: Lightning Pose lists: Customizable Multielectrode Array lists: Live Mouse Tracker Toolkit Analysis lists: HFOApp lists: Synaptic Vesicles Detection lists: Pipette Finding CNN lists: 3DP Gustometer lists: SEB3R lists: Lickometer Box lists: Custom-fitting-of-implants lists: Markerless Mouse Tracking for Social Experiments lists: FARESHARE lists: HERBs lists: E-Scope lists: PyBehave lists: ReachOut lists: One-rat Turnstile lists: TD_Drive lists: Holeboard lists: SaLSa lists: ghostipy lists: DREAM implant lists: HSSM lists: High-Precision Optical Fiber-Based Lickometer lists: NC4gate lists: ArUco lists: STPoseNet lists: Bell Jar lists: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats lists: Active Commutator |
Public | SCR_015938 | 2026-08-15 11:29:55 | 5 | |||||||||
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Boruta Resource Report Resource Website 10+ mentions |
Boruta (RRID:SCR_016234) | algorithm resource, software resource | Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows). | feature, selection, algorithm, wrapper, estimation, shadow, copy | uses: R Project for Statistical Computing | Free, Available to download | https://mbq.github.io/Boruta/ | SCR_016234 | Boruta algorithm, Boruta: Wrapper Algorithm for All Relevant Feature Selection | 2026-08-15 11:30:05 | 11 | ||||||||
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Stim2 Resource Report Resource Website 1+ mentions |
Stim2 (RRID:SCR_016751) | software application, software resource | Software environment for custom stimulus and task design as well as presentation. Compumedics Neuroscan’s design system which can be integrated in fMRI, MEG, and other functional neuro-imaging applications. Provides interface to design and present visual and auditory stimulation paradigms. | Compumedics Neuroscan, stimulus, task, design, presentation, fMRI, MEG, neuroimaging, visual, auditory | Commercially available | SCR_016751 | 2026-08-15 11:30:04 | 3 | |||||||||||
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MIIVsem Resource Report Resource Website |
MIIVsem (RRID:SCR_017444) | software application, data analytics software, software resource | Software R package for estimating structural equation models using instrumental variables. | Estimating, structural, equation, model, instrumental, variable, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
Free, Available for download, Freely available | https://github.com/zackfisher/MIIVsem | SCR_017444 | Model Implied Instrumental Variable Estimation of Structural Equation Models | 2026-08-15 11:29:57 | 0 | ||||||||
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Lenntech activity coefficient calculator Resource Report Resource Website 1+ mentions |
Lenntech activity coefficient calculator (RRID:SCR_016475) | software application, software resource | Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water. | program, calculate, activity, coefficient, ion, solution, strength, concentration, drinking, water, Lenntech | Free, Public | SCR_016475 | 2026-08-15 11:29:57 | 2 | |||||||||||
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Chromeleon Chromatography Data System (CDS) Software Resource Report Resource Website 10+ mentions |
Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) | CDS | software toolkit, software resource | Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results. | Thermofisher, system, chromatography, operation, data, quality, manage, analytical, process, instrument, control | Commercially available | SCR_016874 | Chromeleon Chromatography Data System, Chromeleon Chromatography Data System (CDS), Dionex Chromeleon7 | 2026-08-15 11:30:04 | 11 | |||||||||
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spm_auto_reorient_coregister Resource Report Resource Website |
spm_auto_reorient_coregister (RRID:SCR_017281) | software toolkit, software resource | Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12. | Nifti Libraries, NeuroImaging, MRI, MRI 3D image, reorientation, coregistration, statistical, parametric, mapping | works with: SPM | FNRS 1124417F | Free, Available for download, Freely available | SCR_017281 | 2026-08-15 11:30:06 | 0 | |||||||||
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DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software toolkit, software resource | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-08-15 11:29:57 | 2 | ||||||||
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Scope Resource Report Resource Website 10+ mentions |
Scope (RRID:SCR_017454) | software application, software resource | Two photon microscope control software with multi area capabilities. | Two, photon, microscope, control, BRAIN Initiative | is recommended by: BRAIN Initiative | NINDS NS090475 | Free, Available for download, Freely available | SCR_017454 | 2026-08-15 11:30:05 | 15 | |||||||||
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pyRayleighCuda Resource Report Resource Website |
pyRayleighCuda (RRID:SCR_017453) | software application, software resource | Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation. | Rayleigh-Sommerfeld, integral, acoustics, CUDA, graphics, processing, unit, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH109105 | Free, Freely available | SCR_017453 | 2026-08-15 11:29:58 | 0 | |||||||||
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PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Kavli Foundation ; General Electric ; Howard Hughes Medical Institute ; Allen Institute for Brain Science ; NSF 0855272; International Neuroinformatics Coordinating Facility ; NIH BRAIN Initiative R24 MH116922 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-08-15 11:30:06 | 4 | ||||||
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Libeep EEGLAB plugin Resource Report Resource Website 1+ mentions |
Libeep EEGLAB plugin (RRID:SCR_016334) | software toolkit, software application, software resource | Software as an EEGLAB tool used for LIBEEP recordings. | plugin, library, recording, electrophysiological, data, neuroscience |
is related to: LIBEEP is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016334 | ANTeepimport | 2026-08-15 11:29:56 | 1 | |||||||||
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viridis Resource Report Resource Website 10+ mentions |
viridis (RRID:SCR_016696) | software toolkit, software resource | Software package which brings to R color scales. Created for the Python matplotlib library. | R, color, scale, Python, matplotlib, CRAN |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://github.com/sjmgarnier/viridis | SCR_016696 | 2026-08-15 11:29:57 | 30 | |||||||||
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Referral Center for Animal Models of Human Genetic Diseases Resource Report Resource Website |
Referral Center for Animal Models of Human Genetic Diseases (RRID:SCR_016453) | biomaterial supply resource, material resource | Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients. | animal, dog, cat, disease, homologue, genetic, colony, breed, model | has parent organization: University of Pennsylvania; Philadelphia; USA | NIH Office of the Director P40 OD011189 | SCR_016453 | University of Pennsylvania School of Veterinary Medicine Referral Center for Animal Models of Human Genetic Diseases, UPenn Referral Center for Animal Models of Human Genetic Diseases, PennVet Referral Center for Animal Models of Human Genetic Diseases | 2026-08-15 11:30:04 | 0 |
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