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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:05 | 141 | |||||||||
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MicroDynamix Resource Report Resource Website 1+ mentions |
MicroDynamix (RRID:SCR_017671) | software application, data processing software, software resource, image analysis software, image reconstruction software | Software tool for dendritic spine analysis that enables to visualize and quantify spine morphology over time. After loading image data acquired at different time points from in vivo and in vitro imaging sessions, automatically aligns images in 3D, then reconstructs dendritic branches, detects dendritic spines, and identifies important metrics such as length, thickness, and overall number, for accurate quantitative comparison. | MBF Bioscience, dendritic, spine, analysis, visualize, quantify, morphology, image, data, 3D, reconstruct | Restricted | SCR_017671 | 2026-02-15 09:21:24 | 1 | |||||||||||
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Vesalius Resource Report Resource Website |
Vesalius (RRID:SCR_017670) | software application, data processing software, software resource, data acquisition software, image analysis software, image acquisition software | Software tool as ultra fast, multi channel resonant scanning laser confocal microscope system for rapid 2D and 3D slide scanning, and cleared tissue imaging. System for imaging of slide mounted specimens and cleared tissue imaging. Utilizes strip mosaic scanning process to rapidly and accurately collect fluorescent image data while stage moves specimen continuously in y-axis. | MBF Bioscience, resonant, scanning, laser, confocal, microscope, system, 2D, 3D, slide, cleared, tissue, imaging, collect, fluorescent, image, data, | Restricted | SCR_017670 | 2026-02-15 09:22:05 | 0 | |||||||||||
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Nextstrain Resource Report Resource Website 100+ mentions |
Nextstrain (RRID:SCR_018223) | project portal, data or information resource, data set, portal | Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools. | Pathogen genome data, data, analytic tool, visualization tool, epidemiology, outbreak response |
is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Global Initiative on Sharing All Influenza Data |
COVID-19 | Free, Freely available | https://nextstrain.org/ncov/global | SCR_018223 | nextstrain.org | 2026-02-15 09:22:11 | 273 | |||||||
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Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:11 | 28 | |||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | web service, data access protocol, software resource | 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 | 2026-02-15 09:22:11 | 138 | |||||
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Proteomic Data Commons Resource Report Resource Website 50+ mentions |
Proteomic Data Commons (RRID:SCR_018273) | PDC | database, service resource, storage service resource, data repository, production service resource, data or information resource, analysis service resource | Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication. | Cancer, proteomic, data, precision medicine, diagnosis, treatment, analysis, biospeciment, clinical data, metadata |
is related to: Cancer Research Data Commons has parent organization: National Cancer Institute |
cancer | Restricted | SCR_018273 | 2026-02-15 09:21:34 | 66 | ||||||||
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Drishti Resource Report Resource Website 10+ mentions |
Drishti (RRID:SCR_017999) | software application, data visualization software, data processing software, 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 | 2026-02-15 09:22:09 | 19 | |||||||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | software application, data visualization software, data processing software, software resource, data analysis 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 | 2026-02-15 09:22:18 | 11 | ||||||||||
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Velocyto Resource Report Resource Website 100+ mentions |
Velocyto (RRID:SCR_018167) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:19 | 137 | |||||||||
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astroML Resource Report Resource Website |
astroML (RRID:SCR_018138) | software application, data visualization software, data processing software, software resource, data set, data or information resource, software toolkit, data analysis software | 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 | 2026-02-15 09:22:18 | 0 | |||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | software application, data processing software, software resource, alignment software, 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 | 2026-02-15 09:22:18 | 14 | ||||||||
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Global Initiative on Sharing All Influenza Data Resource Report Resource Website 1000+ mentions |
Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) | GISAID | portal, database, data or information resource, topical portal, disease-related portal | Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data. | hCoV19, hCoV-19 genome sequence, data, coronavirus, SARS coronavirus, Coronavirus, genome, genome database, influenza, SARS-CoV infection, SARS-CoV-2, COVID-19 |
lists: Health Data Research UK COVID-19 Initiative is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Nextstrain |
CoV19, COVID19, COVID-19 | PMID:28382917 | Restricted | SCR_018279, r3d100010126, SCR_018318 | https://doi.org/10.17616/R3Q59F | SCR_018251 | 2026-02-15 09:22:12 | 1964 | |||||
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LibreOfficeCalc Resource Report Resource Website 10+ mentions |
LibreOfficeCalc (RRID:SCR_018013) | data management software, software application, data visualization software, data processing software, software resource, data analysis 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 | 2026-02-15 09:22:18 | 24 | |||||||||||
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COVID-19 Crowd Generated Gene and Drug Set Library Resource Report Resource Website 1+ mentions |
COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) | database, software resource, data access protocol, web service, service resource, storage service resource, data repository, data or information resource | Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community. | COVID-19 data collection, gene collection, drug set collection, data, COVID-19 | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | COVID-19, COVID19 | Free, Freely available | https://github.com/MaayanLab/covid19_crowd_library | SCR_018252 | 2026-02-15 09:22:12 | 3 | ||||||||
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astropy Resource Report Resource Website 10+ mentions |
astropy (RRID:SCR_018148) | software library, portal, software resource, project portal, data or information resource, software toolkit | 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 | 2026-02-15 09:22:19 | 12 | ||||||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software application, data processing software, software resource, software toolkit, data analysis software | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-02-15 09:22:18 | 2 | |||||
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GLYCAM-Web Resource Report Resource Website 50+ mentions |
GLYCAM-Web (RRID:SCR_018260) | portal, software resource, data access protocol, web service, data or information resource, topical portal | Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates. | Glycosylated SARS-Cov-2 Spike protein, SARS-Cov-2, SARS-Cov-2 Spike protein, spike protein, 3D structure, carbohydrate, oligosaccharide conformation, modeling, structure modeling, data | has parent organization: University of Georgia; Georgia; USA | COVID-19, COVID19 | NIH | Free, Freely available | SCR_018260 | GLYCAM | 2026-02-15 09:22:12 | 96 | |||||||
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NCGC CurveFit Resource Report Resource Website 1+ mentions |
NCGC CurveFit (RRID:SCR_018079) | software application, data processing software, software resource, standalone software, data analysis software | Large scale dose response curve fitting and curve classification software. Automated curve fitting and classificatoin software. Web deployed software. Algorithm recognizes bell shaped curves, implements standard hill equation, extensible for other models. | Dose response curve, curve fitting, curve classification, automated, bell shaped curve, standard hill equation, data | Free, Available for download, Freely available | SCR_018079 | 2026-02-15 09:21:31 | 2 | |||||||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data visualization software, data processing software, software resource, data analysis software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-02-15 09:22:10 | 1 |
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