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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software toolkit, software resource | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-08-09 09:08:56 | 84 | ||||||||
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classInt Resource Report Resource Website 1+ mentions |
classInt (RRID:SCR_024515) | software toolkit, software resource | Software R package for choosing univariate class intervals for mapping or other graphics purposes. | choosing univariate class intervals, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/r-spatial/classInt/ | SCR_024515 | Class Intervals | 2026-08-09 09:08:56 | 2 | ||||||||
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mitml Resource Report Resource Website 1+ mentions |
mitml (RRID:SCR_024516) | software toolkit, software resource | Software R package for multiple imputation of missing data in multilevel modeling. | multiple imputation of missing data in multilevel modeling, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/simongrund1/mitml | SCR_024516 | 2026-08-09 09:08:29 | 1 | |||||||||
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Four-dimensional Ascidian Body Atlas Resource Report Resource Website 1+ mentions |
Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) | FABA | data or information resource, atlas, d spatial image | Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate. | gene expression, genome, comparative genomics, human, microarray data, model organism, vertebrate, development, ascidian, embryonic development, embryo, video, developmental stage, 3d, slice, timelapse, egg, larva, time, confocal laser scanning microscopy | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD ; Japan Society for the Promotion of Science 18770207 |
PMID:17557317 | Free, Freely Available | nif-0000-02529 | http://ciona.lab.nig.ac.jp/ascidian/top.html | SCR_001691 | FABA: Four-dimensional Ascidian Body Atlas | 2026-08-09 09:03:14 | 5 | |||||
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ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-08-09 09:02:54 | 0 | |||||||
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Colin 3T/7T High-resolution Atlas Resource Report Resource Website |
Colin 3T/7T High-resolution Atlas (RRID:SCR_000160) | Colin 3T/7T High-resolution Atlas | data or information resource, atlas | High-field extension of the Colin27 single-subject atlas with additional high-resolution, quantitative, averaged scans at both 3T and 7T. | nifti-1, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_157729 | SCR_000160 | Colin 3T / 7T High-resolution Atlas | 2026-08-09 09:02:55 | 0 | |||||||
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EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) | EPMBA | data or information resource, atlas | The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07). | embryonic, brain, c57bl/6j, coronal, developing, developmental, gestational, head, horizontal sections, image, mouse, prenatal | has parent organization: East Tennessee State University; Tennessee; USA | Human Brain Project ; NIMH 263-MD-414639 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10452 | SCR_001882 | EPMBA.org, Electronic Prenatal Mouse Brain Atlas | 2026-08-09 09:03:18 | 1 | ||||||
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Spinal Research Resource Report Resource Website 1+ mentions |
Spinal Research (RRID:SCR_000701) | ISRT | institution | Spinal Research committed to funding international research into cure for spinal cord paralysis. Charity that funds medical research for treating and curing spinal cord paralysis. Supports basic science, clinical research and funds PhD students. ISRT also hosts Annual Network Meetings. | spinal, research, grant, funding, clinical, trust | grid.468536.a, ISNI: 0000 0000 9820 9830, SCR_002736, nif-0000-00473, nif-0000-24038, Crossref funder ID: 501100000334 | https://ror.org/042szwr56 | SCR_000701 | International Spinal Research Trust | 2026-08-09 09:03:02 | 1 | ||||||||
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Images of the Drosophila Nervous System Resource Report Resource Website |
Images of the Drosophila Nervous System (RRID:SCR_000211) | data or information resource, atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Drosophila neurobiology with 3D images, enhancer traps, Golgi impregnations and protocols. This data contains a schematic view onto the brain of an adult fly is a clickable imagemap. The set of links overlaps with those of the 3D-clickable version, but is not identical. | drosphila, fly, invertebrate | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12508 | SCR_000211 | IDNS | 2026-08-09 09:02:55 | 0 | ||||||||
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L-Neuron Resource Report Resource Website 1+ mentions |
L-Neuron (RRID:SCR_014132) | simulation software, software application, software resource | A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth. | simulation softare, virtual neuron, neuronal modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: George Mason University; Virginia; USA |
Available to the research community | http://krasnow1.gmu.edu/cn3/L-Neuron/home.htm | SCR_014132 | L Neuron | 2026-08-09 09:06:17 | 5 | ||||||||
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CSIM Resource Report Resource Website 10+ mentions |
CSIM (RRID:SCR_014256) | simulation software, software application, software resource | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site. | simulation software, circuit simulator, heterogeneous network, object oriented design | is related to: PCSIM | Available for download | SCR_014256 | Circuit SIMulator, CSIM: A neural Circuit SIMulator | 2026-08-09 09:06:22 | 11 | |||||||||
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Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) Resource Report Resource Website |
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) (RRID:SCR_014178) | VERTEX | simulation software, software application, software resource | A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls. | simulation software, matlab, extracellular potential, spiking neural network model, snn model |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24863422 | Available to the research community | SCR_014178 | Virtual Electrode Recording Tool for EXtracellular potentials | 2026-08-09 09:06:18 | 0 | |||||||
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BioPSE Resource Report Resource Website |
BioPSE (RRID:SCR_014044) | simulation software, software application, software resource | A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems. | software, algorithm, simulation, modeling, visaulization, bioelectric field, tool |
is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NIH | Public | SCR_014044 | SCIRun/BioPSE | 2026-08-09 09:06:20 | 0 | ||||||||
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NeoCortical Simulator Resource Report Resource Website |
NeoCortical Simulator (RRID:SCR_014257) | NCS | simulation software, software application, software resource | A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS. | simulation software, neural simulator, conductance based synapse, neurobiotics | has parent organization: University of Nevada at Reno; Nevada; USA | Source code is available | SCR_014257 | 2026-08-09 09:06:20 | 0 | |||||||||
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SimThyr Resource Report Resource Website 10+ mentions |
SimThyr (RRID:SCR_014351) | simulation software, software application, software resource | Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis. | thyroid, homeostasis, simulation, software, modelling, pituitary, model |
is related to: SimulaBeta has parent organization: Ludwig-Maximilians-University; Munich; Germany has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany |
PMID:23365787 DOI:10.1080/01969720490443354 DOI:10.1155/2012/351864 DOI:10.5281/zenodo.1303822 |
Free, Available for download, Freely available | DOI:10.5281/zenodo.1303822 | https://doi.org/10.5281/zenodo.1303822 | SCR_014351 | 2026-08-09 09:06:22 | 11 | |||||||
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Desmond Resource Report Resource Website 500+ mentions |
Desmond (RRID:SCR_014575) | simulation software, software application, software resource | Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer. | simulation, supercomputer, commodity cluster, gpu, parallel algorithm, biological system, parallel algorithms, computer, processor | is used by: CHARMM-GUI | Open source, Free for non-commercial use, Commercial entities must contact Schrodinger LLC | SCR_014575 | 2026-08-09 09:06:27 | 946 | ||||||||||
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Tool for Tumor Progression Resource Report Resource Website 1+ mentions |
Tool for Tumor Progression (RRID:SCR_014700) | TTP | simulation software, software application, software resource | Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above. | tumor, tumor progression, cancer, simulation, simulation software, tumor dynamics, tumor growth | Cancer | Available for download, Necessary libraries are included in the file | SCR_014700 | Tool for Tumor Progression (TTP) | 2026-08-09 09:06:27 | 1 | ||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software application, software resource | Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. | simulation software, simulator, java, neuronal signaling pathway, neuron | HFSP ; NIMH K21-MH01141; NSF IBN 0077509; CRCNS program R01 AA16022; CRCNS program AA18066 |
Available for download | https://github.com/neurord/stochdiff/releases | SCR_014769 | 2026-08-09 09:06:31 | 13 | |||||||||
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COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software application, software resource | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | 2026-08-09 09:06:11 | 51 | ||||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | simulation software, software application, software resource | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI. | simulation software, simulator, heterogenous network, model, neuron, synapse | is related to: CSIM | DOI:10.3389/neuro.11.011.2009 | Available for download | SCR_014770 | Parallel neural Circuit SIMulator, Parallel Neural Circuit Simulator (PCSIM), Parallel Neural Circuit Simulator | 2026-08-09 09:06:11 | 4 |
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