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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-08-01 12:05:43 | 8 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | software resource, software application, image processing software, data processing software | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-08-01 12:05:44 | 64 | ||||
|
GCTF Resource Report Resource Website 100+ mentions |
GCTF (RRID:SCR_016500) | GCTF | data processing software, data analysis software, software application, software resource | Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | accurate, real, time, constrast, transfer, function, determination, correction, atomic, resolution, cryo, electron, microscopy, reconstruction, micrograph | is related to: University of Cambridge; Cambridge; United Kingdom | the Medical Research Council ; United Kingdom MC_UP_A025_1011; Wellcome Trust New Investigator Award |
PMID:26592709 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016500 | GContrast Transfer Function | 2026-08-01 12:05:40 | 100 | ||||||
|
MIRRI Resource Report Resource Website 1+ mentions |
MIRRI (RRID:SCR_016461) | MIRRI | biobank, material storage repository, data or information resource, storage service resource, portal, data access protocol, database, service resource, topical portal, software resource, organization portal, european biobank, organism-related portal, web service | Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application. | European, research, infrastructure, microbial, resource, database, service, stock, center | the European Commission 312251; the European Union’s Seventh Framework Programme 312251 |
Free, Freely available | SCR_016461 | Microbal Resource Research Infrastructure | 2026-08-01 12:05:42 | 9 | ||||||||
|
Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, portal, database, topical portal, organism-related portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-08-01 12:05:42 | 5 | |||||
|
iMaps Resource Report Resource Website 1+ mentions |
iMaps (RRID:SCR_016705) | data analysis service, data or information resource, portal, service resource, production service resource, analysis service resource | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-08-01 12:05:39 | 9 | ||||||||||
|
Zeiss: libra 120 transmission electron microscope Resource Report Resource Website 1+ mentions |
Zeiss: libra 120 transmission electron microscope (RRID:SCR_016703) | instrument resource | Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system. | instrument, electron, microscope, Carl Zeiss | Commercially available | https://drive.google.com/file/d/1sgiYV8KlKkLXagtcEe1d-Oh7y0_GncP6/view?usp=drivesdk | https://www.binran.ru/files/ckp/tem/CKP_Libra%20120%20en_User%20Manual.pdf | SCR_016703 | Carl Zeiss AG - LIBRA 120, libra 120, The LIBRA 120 | 2026-08-01 12:05:51 | 1 | ||||||||
|
Gallios: Flow Cytometer Resource Report Resource Website 1+ mentions |
Gallios: Flow Cytometer (RRID:SCR_016702) | instrument resource | Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs. | instrument, coulter, flow, cytometer, multicolor, assay, cell, processing, parameter, acquisition | Commercially available | https://www.beckman.de/en/coulter-flow-cytometers/gallios/ | SCR_016702 | 2026-08-01 12:05:39 | 1 | ||||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | data analysis service, web application, service resource, production service resource, software resource, analysis service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-08-01 12:05:50 | 22 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data processing software, data analysis software, software application, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-08-01 12:05:42 | 35 | |||||||||
|
Neuronexus: Neural Probe A1x16-3mm-100-703 Resource Report Resource Website |
Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) | instrument resource | Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications. | NeuroNexus, Matrix Array, neural, probe, 16 channel, linear, electrode, array, map, brain, function | Commercially available | http://neuronexus.com/electrode-array/a1x16-3mm-100-703/ | SCR_016678 | 2026-08-01 12:05:42 | 0 | ||||||||||
|
INC-Seq Resource Report Resource Website |
INC-Seq (RRID:SCR_016711) | INC-Seq | data analysis software, software application, software resource, sequence analysis software, data processing software | Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities. | accurate, single, molecule, read, nanopore, sequencing, 16S rRNA, bacteria | is related to: NanoAmpli-Seq | Agency for Science ; Technology and Research ; Singapore |
PMID:27485345 | Free, Available for download, Freely available | https://zenodo.org/record/57405#.W-nb0pNKiM8 | SCR_016711 | Intramolecular ligated Nanopore Consensus Sequencing, INC-Seq | 2026-08-01 12:05:39 | 0 | |||||
|
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator Resource Report Resource Website 1+ mentions |
A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) | instrument resource | Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols. | A-M Systems, stimulation, instrument, neurophysiological, physiological, experiment, protocol | Commercially available | https://drive.google.com/file/d/1sN9NYzMciABPPgk09f3cVZDrhiJfak24/view?usp=drivesdk | https://www.a-msystems.com/pub/manuals/2100manual.pdf | SCR_016677 | 2026-08-01 12:05:38 | 6 | |||||||||
|
NanoAmpli-Seq Resource Report Resource Website 1+ mentions |
NanoAmpli-Seq (RRID:SCR_016710) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. | amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene |
is related to: INC-Seq has parent organization: University of Glasgow; Glasgow; United Kingdom |
EPSRC EP/M016811/1; NERC NE/L011956/1 |
DOI:10.1101/244517 | Free, Available for download, Freely available | https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 | SCR_016710 | 2026-08-01 12:05:51 | 1 | |||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | image analysis software, data visualization software, data analysis software, software application, software resource, data processing software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-08-01 12:05:39 | 5 | ||||||
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Florida State University Physical Biochemistry Core Facility Resource Report Resource Website 1+ mentions |
Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) | PBF | data or information resource, material service resource, narrative resource, service resource, availability annotation standard, standard specification, core facility, production service resource, access service resource, training service resource, the community can contribute to this resource, nif annotation standard | Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students. | core, facility, biophysical, study, macromolecule, providing, resource, instrument, training, guidance, student, Florida, State, University |
has parent organization: Florida State University; Florida; USA has parent organization: Institute of Molecular Biophysics at Florida State University; Florida; USA |
Restricted | SCR_016714 | The Physical Biochemistry Facility (PBF), The Physical Biochemistry Facility, Physical Biochemistry Facility | 2026-08-01 12:05:39 | 1 | ||||||||
|
Columbus Instruments: Oxymax-CLAMS Resource Report Resource Website 100+ mentions |
Columbus Instruments: Oxymax-CLAMS (RRID:SCR_016718) | CLAMS | instrument resource | Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for experiments lasting up to three days. | instrument, monitor, behavior, physiology, lab animal | Commercially available | https://physiology.case.edu/media/eq_manuals/eq_manual_clams_brochure.pdf | http://www.colinst.com/ | SCR_016718 | Comprehensive Lab Animal Monitoring System | 2026-08-01 12:05:51 | 456 | |||||||
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University of FLorida College of Medicine Molecular Pathology Core Facility Resource Report Resource Website 10+ mentions |
University of FLorida College of Medicine Molecular Pathology Core Facility (RRID:SCR_016601) | MPC | core facility, service resource, access service resource | Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays.. | histology, immunohistochemistry, sample processing, clinical research, cryosectioning, imaging, staining, immunfluorescence, microarrays, core facility |
has parent organization: University of Florida Labs and Facilities has parent organization: University of Florida; Florida; USA |
Restricted | SCR_001055, SciEx_8810 | http://www.scienceexchange.com/facilities/molecular-pathology-core-ufl | SCR_016601 | Molecular Pathology Core, , University of Florida Molecular Pathology Core | 2026-08-01 12:05:41 | 13 | ||||||
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BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | data visualization software, data analysis software, software application, software resource, data processing software | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-08-01 12:05:40 | 5 | |||||||||
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VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | data or information resource, data repository, storage service resource, portal, data access protocol, database, service resource, software resource, web service | Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap. | disease, map, collection, data, distribution, model, arthropod, disease, vector, species | has parent organization: Walter Reed Biosystematics Unit | arthropod disease | US Department of Defense Global Emerging Infections Surveillance and Response System ; Division of the Armed Forces Health Surveillance Center ; Global Biodiversity Information System |
Public, Free, Available for download, Freely available, Acknowledgement requested, Tutorial available | SCR_016721 | 2026-08-01 12:05:51 | 22 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
