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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Eukaryotic Promoter Database Resource Report Resource Website 50+ mentions |
Eukaryotic Promoter Database (RRID:SCR_002132) | EPD | database, data or information resource | Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. | Eukaryotic promoters collection, published articles promoter collection, published article, POL II promoter, biiologically meaningful promoter, comparative sequence analysis |
is used by: Transcriptional Regulatory Element Database is related to: EPDnew is related to: EPDnew has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Government ; Swiss National Science Foundation |
PMID:14681364 PMID:23193273 PMID:31680159 |
Free, Freely available | nif-0000-20940 | https://epd.expasy.org/ | SCR_002132 | The Eukaryotic Promoter Database | 2026-08-08 12:03:51 | 60 | ||||
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STIFDB Resource Report Resource Website 10+ mentions |
STIFDB (RRID:SCR_002131) | STIFDB | database, data or information resource | Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method. | stress responsive, transcription factor, biotic, abiotic, gene, transcription factor binding site, promoter, stress, chromosome, blast |
is listed by: OMICtools has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
PMID:23314754 PMID:19841686 |
Free, Freely Available | OMICS_01866 | SCR_002131 | Stress Responsive Transcription Factor Database | 2026-08-08 12:03:39 | 11 | ||||||
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Transcription Factor encyclopedia Resource Report Resource Website 1+ mentions |
Transcription Factor encyclopedia (RRID:SCR_002130) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest. | binding site, regulatory sequence, transcription factor | PMID:22458515 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20924 | SCR_002130 | Tfe | 2026-08-08 12:03:51 | 2 | ||||||||
|
Organelle Genomics Resource Report Resource Website 1+ mentions |
Organelle Genomics (RRID:SCR_002137) | OGMP | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. | genome, mitochondrial dna, mitochondrial genome, organelle | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20928, r3d100010926 | https://doi.org/10.17616/R3TG9G | SCR_002137 | Organelle Genome Megasequencing Program | 2026-08-08 12:03:48 | 2 | |||||||
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WikiPathways Resource Report Resource Website 1000+ mentions |
WikiPathways (RRID:SCR_002134) | database, data or information resource, service resource | Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. | database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is related to: PharmGKB is related to: Reactome is related to: NetPath is related to: ConsensusPathDB is related to: NCBI BioSystems Database is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of California at San Francisco; California; USA has parent organization: Maastricht University; Maastricht; Netherlands |
NIH ; Netherlands Bioinformatics Centre ; Google Summer of Code program ; NWO - Netherlands Organization for Scientific Research ; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:22096230 PMID:18651794 |
Free, Freely available | nif-0000-20925, r3d100013316 | SCR_002134 | Wiki Pathways | 2026-08-08 12:03:39 | 2013 | ||||||
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Protein interaction and molecular information database Resource Report Resource Website |
Protein interaction and molecular information database (RRID:SCR_002096) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible. | eukaryote, kinase pathway, protein, structure | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20899 | http://prime.ontology.ims.u-tokyo.ac.jp:8081/ | SCR_002096 | PRIME | 2026-08-08 12:03:39 | 0 | ||||||||
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Rice Metabolic Pathway Database Resource Report Resource Website 1+ mentions |
Rice Metabolic Pathway Database (RRID:SCR_002128) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP. | gene, biochemical pathway, rice | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20922 | http://www.gramene.org/pathway/ricecyc.html | SCR_002128 | Rice Metabolic Pathways, RiceCyc | 2026-08-08 12:03:39 | 9 | ||||||||
|
pSTIING Resource Report Resource Website 1+ mentions |
pSTIING (RRID:SCR_002045) | pSTIING | database, data or information resource | A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. | protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University College London; London; United Kingdom |
Inflammation, Tumor, Cancer | PMID:16381926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01916 | SCR_002045 | Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway | 2026-08-08 12:03:38 | 2 | |||||
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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 | 2026-08-08 12:00:34 | 1 | ||||||||
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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 | 2026-08-08 12:00:59 | 1 | ||||||||||
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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 | 2026-08-08 12:00:59 | 0 | ||||||||||
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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 | 2026-08-08 12:00:34 | 6 | |||||||||
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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 | 2026-08-08 12:01:00 | 486 | |||||||
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BD Biosciences: FACSAria III Cell Sorter Resource Report Resource Website 100+ mentions |
BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) | instrument resource | Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time. | instrument, equipment, USEDit, BD Biosciences, cell, sorter, positive, air, pressure, force, cell, flow | is listed by: USEDit | Commercially available | https://drive.google.com/file/d/14L46Z9kYGpNi6KVjyhP9KmXogSN7q82n/view?usp=drivesdk | Model_Number_FACSAria_III | https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD-FACSAria-III-Cell-Sorter-Brochure.pdf, https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/FACSDiva_Software_Brochure.pdf | http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-facsaria-iii/m/744763/features | SCR_016695 | BD FACSARIA III cell sorter, BD FACSARIA III | 2026-08-08 12:00:59 | 106 | |||||
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dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | web application, software resource | Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016612 | Desktop cDNA Annotation System | 2026-08-08 12:00:33 | 0 | ||||||||
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Numbers Resource Report Resource Website 1+ mentions |
Numbers (RRID:SCR_016950) | software resource | Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations. | Apple, create, spreadsheet, table, image, diagram, illustration, color | Commercially available | SCR_016950 | 2026-08-08 12:00:39 | 2 | |||||||||||
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Whisker tracking macro Resource Report Resource Website 1+ mentions |
Whisker tracking macro (RRID:SCR_016953) | software resource | ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker. | ImageJ, plugin, macro, whisker, tracking, Fiji, single | is a plug in for: ImageJ | Free, Available for download, Freely available | SCR_016953 | 2026-08-08 12:00:39 | 2 | ||||||||||
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Affinity Photo Resource Report Resource Website 10+ mentions |
Affinity Photo (RRID:SCR_016951) | software resource | Software tool for professional photo editing. | Affinity, professional, photo, editing | Commercially available | SCR_016951 | 2026-08-08 12:00:39 | 35 | |||||||||||
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Olympus: FV1000 Confocal Microscope Resource Report Resource Website 10+ mentions |
Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) | instrument resource | FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels. | FV 1000, confocal, laser, scanning, microscope, spectroscopy, living, intercellular, object, Olympus | is provided by: Olympus | Commercially available | http://olympusconfocal.com/brochures/pdfs/FV1000.pdf | SCR_016840 | 2026-08-08 12:00:36 | 20 | |||||||||
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Leica: CM3050 S Research Cryostat Resource Report Resource Website 10+ mentions |
Leica: CM3050 S Research Cryostat (RRID:SCR_016844) | instrument resource | Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research. | instrument, cryosectioning, biomedical, neuroanatomical, cryostat, Leica, histology, equipment | Commercially available | https://www.leicabiosystems.com/sites/default/files/media_product-download/2022-01/Leica_CM3050S_IFU_2v4N_en.pdf | SCR_016844 | Leica CM3050 cryostat | 2026-08-08 12:01:01 | 27 |
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