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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | web application, sequence analysis software, software resource, software application, data analysis software, data processing software | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-08-08 12:00:32 | 6 | ||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | sequence analysis software, software resource, software application, data analysis software, data analytics software, data processing software | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 355804783; Wellcome Trust WT092340; Wellcome Trust WT083481; Wellcome Trust 106370Z14 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-08-08 12:00:56 | 133 | ||||||||
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miRmap Resource Report Resource Website 100+ mentions |
miRmap (RRID:SCR_016508) | software toolkit, software library, software resource, software application, data analytics software | Software application as an open source Pyton library to search and predict miRNA targets. | search, predict, miRNA, target | is listed by: OMICtools | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:23034802 | Free, Available for download, Freely available, Tutorial available | http://cegg.unige.ch/mirmap | SCR_016508 | 2026-08-08 12:00:32 | 227 | |||||||
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MIMMS microscope 1.0 (2016) Resource Report Resource Website 1+ mentions |
MIMMS microscope 1.0 (2016) (RRID:SCR_016511) | MIMMS | instrument resource | Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications. | instrument, computer, controlled, microscope, two, photon, laser, scanning, imagining | has parent organization: Howard Hughes Medical Institute | Available for Free for non profit research in the Janelia research community | SCR_016511 | Modular In vivo Multiphoton Microscopy System | 2026-08-08 12:00:56 | 7 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | web application, sequence analysis software, software resource, software application, data analysis software, data processing software | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-08-08 12:00:56 | 1 | |||||||
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MetaPGN Resource Report Resource Website 1+ mentions |
MetaPGN (RRID:SCR_016472) | MetaPGN | network graph visualization software, software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | construct, graphical, visualization, annotated, pangenome, network, microbal, genome, metagenome | PMID:30277499 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/peng-ye/MetaPGN | SCR_016472 | Meta PanGeNome | 2026-08-08 12:00:32 | 2 | |||||||
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Thermo Fisher: Nanodrop 1000 Spectrophotometer Resource Report Resource Website 50+ mentions |
Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) | instrument resource | Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution. | ABRF, spectrophotometer, nanodrop, concentration measurement, optical density, DNA, RNA, protein, nanodrop, instrument, equipment |
is listed by: USEDit works with: Thermo Scientific NanoDrop 1000 Software |
Commercially available | https://drive.google.com/file/d/1C1Dj_A1QxQibucCbFNues9EDZebDnx8K/view?usp=drivesdk | SCR_018035, Model_Number_Nanodrop_1000, SCR_020560 | https://www.marshallscientific.com/Nanodrop-ND-1000-Spectrophotometer-p/nd-1000.htm, https://www.selectscience.net/products/nanodrop-1000-spectrophotometer/?prodID=79482#tab-2, http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf | SCR_016517 | NanoDrop 1000, Nanodrop ND-1000, Thermo Scientific NanoDrop 1000, NanoDrop 1000 Spectrophotometer | 2026-08-08 12:00:32 | 89 | ||||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | data or information resource, software resource, software application, source code, database | Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective". | data, code, Phyton, research, paper, probabilistic, neural, network | Free, Available for download, Freely available | SCR_016485 | Probabilistic Neural Networks MiceMachineVision | 2026-08-08 12:00:32 | 2 | |||||||||
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | software resource, data access protocol, web service, service resource | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NHLBI U54 HL127624; NCI U24 CA224260 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-08-08 12:00:32 | 0 | ||||||
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Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-08-08 12:00:56 | 1 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | software toolkit, software resource, software application, data analysis software, data processing software | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | 2026-08-08 12:00:56 | 38 | |||||||||
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Dormed Hellas: Monica AN24 Resource Report Resource Website 1+ mentions |
Dormed Hellas: Monica AN24 (RRID:SCR_016455) | instrument resource | Monitors the electrical signals on the patient’s abdomen by using the abdominal fECG and mECG wave shape to uniquely identify and separate the maternal and fetal heart rates. | Instrument, monitor, electrical, signal, patient, abdoment, separate, maternal, fetal, heart, rate | It has been discontinued | https://drive.google.com/file/d/1Agh-RBIqoW5hWevf4o9B6_dCYEUBsNH_/view?usp=sharing | https://www.accessdata.fda.gov/cdrh_docs/pdf11/K112390.pdf | SCR_016455 | 2026-08-08 12:00:32 | 1 | |||||||||
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NCBI Biocollections Resource Report Resource Website 1+ mentions |
NCBI Biocollections (RRID:SCR_016459) | NCBI Biocollections | data or information resource, registration software, image analysis software, software resource, software application, database, portal, organization portal, data processing software | Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site. | registry, biocollection, linked, genome, dataset, metadata | SCR_016459 | NCBI Biocollections:National Center for Biotechnology Information Biocollections | 2026-08-08 12:00:32 | 2 | ||||||||||
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SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, portal, disease-related portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-08-08 12:00:33 | 0 | ||||||||
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UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, material resource, organism supplier | Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi. | microbial, repository, collection, preservation, analysis, identification, fungi | is related to: University of Toronto; Ontario; Canada | SCR_016466 | 2026-08-08 12:00:55 | 5 | |||||||||||
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NRRL ARS Culture Collection Resource Report Resource Website 10+ mentions |
NRRL ARS Culture Collection (RRID:SCR_016465) | NRRL ARS | biomaterial supply resource, material resource, organism supplier | Center that collects, deposits, maintains bacteria and fungi, and facilitates microbiological research to advance agricultural production, food safety, public health, and economic development. Housed within the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois. | collect, deposit, maintain, facilitate, microbiology, research, agriculture, bacteria, fungi | SCR_016465 | NRRL:Northern Regional Research Laboratory, ARS:Agricultural Research Service | 2026-08-08 12:00:56 | 39 | ||||||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | data or information resource, web service, organism-related portal, software resource, data access protocol, topical portal, database, project portal, portal | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2026-08-08 12:00:32 | 2 | |||||||||
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MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | sequence analysis software, software resource, software application, data 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 | 2026-08-08 12:00:56 | 15 | ||||||
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cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | image processing software, software resource, software application, 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 | 2026-08-08 12:00:32 | 67 | ||||
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GCTF Resource Report Resource Website 100+ mentions |
GCTF (RRID:SCR_016500) | GCTF | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:56 | 101 |
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