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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioWheel Resource Report Resource Website |
BioWheel (RRID:SCR_017441) | data processing software, data visualization software, software application, software resource | Software tool for interactive graphs of high dimensional data. Interactive cloud based software tool by DIBSVIS. | Interactive, graph, high, dimensional, data, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1533708 | Restricted | SCR_017441 | , bio wheel, biowheel | 2026-08-04 09:44:08 | 0 | ||||||||
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ShinyLearner Resource Report Resource Website 1+ mentions |
ShinyLearner (RRID:SCR_017608) | data processing software, software application, software resource, data analysis software | Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data. | Benchmark, machine, learning, classification, algorithm, tabular, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/675181 | Free, Available for download, Freely available | biotools:ShinyLearner | https://bio.tools/ShinyLearner | SCR_017608 | 2026-08-04 09:44:15 | 2 | |||||||
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Silver Lab Microscopy Software Resource Report Resource Website 1+ mentions |
Silver Lab Microscopy Software (RRID:SCR_017456) | data processing software, software resource, software application, data visualization software, data acquisition software | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | Imaging, visualising, electrophysiological, data, acousto, optic, lens, microscope, Silver Lab, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University College London; London; United Kingdom |
NINDS NS099689 | Free, Available for download, Freely available | http://silverlab.org/software-resources/ | SCR_017456 | 2026-08-04 09:44:13 | 2 | ||||||||
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Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | web service, storage service resource, software resource, data access protocol, data repository, service resource | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-08-04 09:44:09 | 1 | |||||
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | data processing software, software application, software resource, data analysis software | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-08-04 09:44:13 | 13 | ||||||||
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Inorganic Crystal Structure Database (ICSD) Resource Report Resource Website 1+ mentions |
Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) | ICSD | storage service resource, data repository, service resource, database, data or information resource | Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research. | Inorganic, crystal, structure, data, atomic, coordinate, quality, FIZ Karlsruhe — Leibniz Institute for Information Infrastructure |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Restricted | r3d100010085 | http://www2.fiz-karlsruhe.de/icsd_home.html, https://doi.org/10.17616/R3GW2V | SCR_017429 | Inorganic Crystal Structure Database, Inorganic Crystal Structure Database (ICSD), ICSD | 2026-08-04 09:44:10 | 6 | ||||||
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vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | data processing software, software application, software resource, data analysis software | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-08-04 09:44:14 | 3 | ||||||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | simulation software, data processing software, data analysis software, software resource, software application | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | 2026-08-04 09:44:08 | 13 | |||||
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LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | data processing software, software application, software resource, data analysis software | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-08-04 09:44:14 | 141 | |||||||||
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Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data processing software, software application, software resource, data analysis software | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | 2026-08-04 09:44:21 | 28 | |||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, software resource, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-08-04 09:44:18 | 138 | |||||
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Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | storage service resource, data repository, service resource, database, data or information resource | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | MouseBytes | 2026-08-04 09:44:14 | 4 | |||||
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Drishti Resource Report Resource Website 10+ mentions |
Drishti (RRID:SCR_017999) | data processing software, data visualization software, software application, software resource | Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc. | Visualization, volumetric data, tomography, electron microscopy, data | Free, Available for download, Freely available | SCR_017999 | 2026-08-04 09:44:16 | 19 | |||||||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | data processing software, data analysis software, software resource, software application, data visualization software | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-08-04 09:44:19 | 11 | ||||||||||
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Velocyto Resource Report Resource Website 100+ mentions |
Velocyto (RRID:SCR_018167) | data processing software, software application, software resource, data analysis software | Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R. | Expression dynamic, single cell RNAseq data, data, RNAseq, RNA velocity, mRNA, RNAseq dataset, estimation RNA velocity | Free, Available for download, Freely available | https://github.com/velocyto-team/velocyto.py, https://github.com/velocyto-team/velocyto.R | SCR_018167 | velocyto.py, velocyto, velocyto.R | 2026-08-04 09:44:17 | 137 | |||||||||
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astroML Resource Report Resource Website |
astroML (RRID:SCR_018138) | data processing software, data analysis software, data set, software resource, software application, data visualization software, software toolkit, data or information resource | Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics. | Machine learning, statistics, data mining, data, astronomy, astrophysics, data analysis | DOI:10.1109/CIDU.2012.6382200 | Free, Available for download, Freely available | https://github.com/astroML/astroML/blob/master/doc/index.rst | SCR_018138 | 2026-08-04 09:44:20 | 0 | |||||||||
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webchem Resource Report Resource Website 1+ mentions |
webchem (RRID:SCR_017684) | data processing software, software application, software resource, data acquisition software | Open source software package for R programming language that is used to acquire chemical information from online data sources. Package contains functions that allow programmer to interact with webpages and APIs to retrieve chemical information. | R programming language, acquire, chemical, information, online, data, retrive | is listed by: CRAN | Free, Available for download, Freely available | https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem | SCR_017684 | Chemical Information from Web | 2026-08-04 09:44:12 | 1 | ||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | data processing software, alignment software, software resource, software application, image analysis software | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-08-04 09:44:20 | 14 | ||||||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | data processing software, data analysis software, data management software, software resource, software application, data visualization software | Open source software application with data analysis tools and spreadsheet templates used to manage, process and visualize data. LibreOffice Calc is spreadsheet component of LibreOffice software package developed by Document Foundation. | Data, analysis, spreadsheet, template, process, visualize | Free, Available for download, Freely available | SCR_018013 | 2026-08-04 09:44:15 | 24 | |||||||||||
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astropy Resource Report Resource Website 10+ mentions |
astropy (RRID:SCR_018148) | portal, software resource, software library, project portal, software toolkit, data or information resource | Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis. | Astronomy, domain specific file format, flexible image transport system file, virtual observatory table, physical quantity conversion, unit conversion, celestial coordinate, data, cosmological transformation framework, cosmological conversion framework | DOI:10.3847/1538-3881/aabc4f DOI:10.1051/0004-6361/201322068 |
Free, Available for download, Freely available | SCR_018148 | 2026-08-04 09:44:16 | 12 |
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