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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bootstrap CSS Resource Report Resource Website 10+ mentions |
Bootstrap CSS (RRID:SCR_016096) | software resource, programming language | 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 | 2026-08-17 09:35:36 | 11 | |||||||||
|
Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | software resource, standalone software, software application | 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 | 2026-08-17 09:35:33 | 6 | ||||||
|
Stim2 Resource Report Resource Website 1+ mentions |
Stim2 (RRID:SCR_016751) | software resource, software application | 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 | 2026-08-17 09:35:54 | 3 | |||||||||||
|
Lenntech activity coefficient calculator Resource Report Resource Website 1+ mentions |
Lenntech activity coefficient calculator (RRID:SCR_016475) | software resource, software application | 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 | 2026-08-17 09:35:45 | 2 | |||||||||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software resource, software application | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-08-17 09:36:10 | 5 | |||||
|
Scope Resource Report Resource Website 10+ mentions |
Scope (RRID:SCR_017454) | software resource, software application | 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 | 2026-08-17 09:35:56 | 15 | |||||||||
|
pyRayleighCuda Resource Report Resource Website |
pyRayleighCuda (RRID:SCR_017453) | software resource, software application | 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 | 2026-08-17 09:36:12 | 0 | |||||||||
|
PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software resource, software application | 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 | 2026-08-17 09:35:55 | 4 | ||||||
|
Condor Resource Report Resource Website 1+ mentions |
Condor (RRID:SCR_017664) | software resource, software application | Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid. | GRID computing software, Distributed Computing Engine, computing, system, maintain, distribute, support | has parent organization: California Institute of Technology; Pasadena; USA | DOI:10.1002/cpe.938 | Free, Freely available | https://research.cs.wisc.edu/htcondor/manual/v7.8/index.html | SCR_017664 | 2026-08-17 09:36:01 | 7 | ||||||||
|
BioBERT Resource Report Resource Website 50+ mentions |
BioBERT (RRID:SCR_017547) | software resource, software application | Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. | Pretrained, biomedical, language, representation, model, text, mining, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BERT |
National Research Foundation of Korea | DOI:10.1093/bioinformatics/btz682 | Free, Available for download, Freely available | biotools:biobERt | https://github.com/naver/biobert-pretrained, https://bio.tools/BioBERT | SCR_017547 | Bidirectional Encoder Representations from Transformers for Biomedical Text Mining | 2026-08-17 09:36:12 | 56 | |||||
|
nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software resource, software application | Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. | Jupyter, notebook, extension, docker, container, code, computing, environment, data | is related to: University of Washington; Seattle; USA | NHLBI U54 HL127624; NIGMS R01 GM126019; Institute of Technology at University of Washington Tacoma |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | 2026-08-17 09:35:49 | 0 | |||||||
|
MixitWin Resource Report Resource Website |
MixitWin (RRID:SCR_017553) | software resource, software application | Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species. | Professional, feed, formulation, Agricultural Software Consultants Inc., | Restricted | SCR_017553 | Mixit-Win | 2026-08-17 09:36:12 | 0 | ||||||||||
|
HomoeologPrimer Resource Report Resource Website 1+ mentions |
HomoeologPrimer (RRID:SCR_017559) | software resource, software application | Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs. | Design, primer, homoeolog, amplify | Free, Available for download, Freely available | SCR_017559 | 2026-08-17 09:36:12 | 1 | |||||||||||
|
Google Sheets Resource Report Resource Website 10+ mentions |
Google Sheets (RRID:SCR_017679) | software resource, software application | Spreadsheet program included as part of free, web-based software office suite offered by Google within its Google Drive service. Service also includes Google Docs and Google Slides, word processor and presentation program respectively. | Spreadsheet, program, office, suite, Google, Drive, service | Free, Available for download, Freely available | SCR_017679 | Spreadsheets | 2026-08-17 09:36:01 | 21 | ||||||||||
|
SQLite Resource Report Resource Website 50+ mentions |
SQLite (RRID:SCR_017672) | software resource, software application | Relational database management system contained in C library. SQLite is not client server database engine but it is embedded into the end program. | Database, management, system, C library, engine, embedded, the end program | is listed by: SoftCite | Free, Freely available | SCR_017672 | 2026-08-17 09:35:57 | 83 | ||||||||||
|
EEGsynth Resource Report Resource Website 1+ mentions |
EEGsynth (RRID:SCR_018732) | software resource, software application | Open source Python codebase that provides real-time interface between open-hardware devices for electrophysiological recordings like EEG, EMG, and ECG, and analog and digital devices like MIDI, OSC, and analog synthesizers. This allows one to use electrical brain/body activity to flexibly control devices in real-time. | Codebase, electrophysiological recording, interface, analog, digital device, analog synthesizer, device control, electrical brain activity, EEG, EMG, ECG, BCI, Neurofeedback, Biofeedback, Music, MIDI, OSC, Python | Free, Freely available | https://www.eegsynth.org, http://pypi.org/project/eegsynth/ | SCR_018732 | 2026-08-17 09:36:11 | 2 | ||||||||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software resource, software application | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-08-17 09:36:17 | 2 | ||||||
|
eido Resource Report Resource Website 1+ mentions |
eido (RRID:SCR_021076) | software resource, software application | Software validation tool for Portable Encapsulated Projects or PEPs in python. | validation tool, Portable Encapsulated Projects, PEPs, python | is related to: peppy | DOI:10.1101/2020.10.08.331322 | Free, Available for download, Freely available | https://github.com/pepkit/eido/ | SCR_021076 | 2026-08-17 09:36:41 | 1 | ||||||||
|
ACD/ChemSketch Resource Report Resource Website 10+ mentions |
ACD/ChemSketch (RRID:SCR_019272) | software resource, software application | Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease. | Chemical structure, molecular structure, drawing application, generate molecular structure names, calculate molecular properties, create professional reports, ACD Labs | Restricted | SCR_019272 | ChemSketch | 2026-08-17 09:36:30 | 22 | ||||||||||
|
Perl Programming Language Resource Report Resource Website 100+ mentions |
Perl Programming Language (RRID:SCR_018313) | software resource, programming language | Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019. | Programming language | Free, Available for download, Freely available | SCR_018313 | Perl 5, Perl 6, Raku | 2026-08-17 09:36:06 | 382 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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