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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Natural Scenes Dataset Resource Report Resource Website 10+ mentions |
Natural Scenes Dataset (RRID:SCR_023648) | NSD | topical portal, data or information resource, data set, portal | Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry. | Natural scenes, vision, fMRI measurements, fMRI dataset, whole brain, healthy adult subjects, images, visual representation and cognition, benchmark, training data | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | PMID:34916659 | Free,Freely available | https://github.com/cvnlab/nsdcode/ | SCR_023648 | 2026-08-13 09:30:48 | 44 | |||||||
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SlideBook Resource Report Resource Website 500+ mentions |
SlideBook (RRID:SCR_014423) | data analysis software, data processing software, software resource, software application | Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton. | SCR_014423 | 2026-08-13 09:29:03 | 986 | |||||||||||||
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loadGffToGe_db for custom genome Resource Report Resource Website 1+ mentions |
loadGffToGe_db for custom genome (RRID:SCR_015997) | data processing software, software resource, data visualization software, software application | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE. | Next Generation Sequencers, Next Generation Sequencers data, Next Generation Sequencers data analysis and visualization, | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | https://cell-innovation.nig.ac.jp/maser/index_en.html | SCR_015997 | Management and Analysis System for Enormous Reads: loadGffToGe_db for custom genome | 2026-08-13 09:29:32 | 1 | ||||||||
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vhlab-TwoPhoton-matlab Resource Report Resource Website 1+ mentions |
vhlab-TwoPhoton-matlab (RRID:SCR_023369) | data analysis software, data processing software, software resource, software application | Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab. | Matlab, calcium imaging data analysis, calcium imaging, images, time series data extraction, | PMID:18946471 | Free, Available for download, Freely available | SCR_023369 | Van Hooser lab fluorescent time-series analysis software | 2026-08-13 09:30:44 | 2 | |||||||||
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MetGENE Resource Report Resource Website 1+ mentions |
MetGENE (RRID:SCR_023402) | data access protocol, software resource, web service | Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype. | Gene centric metabolomics information retrieval, genes and metabolites associations identification, gene centric data aggregator, | has parent organization: University of California at San Diego; California; USA | NIH Common Funds | Free, Freely available | https://bdcw.org/MW/docs/MetGENETutorial.pdf | SCR_023402 | 2026-08-13 09:31:04 | 1 | ||||||||
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partec flomax Resource Report Resource Website 1+ mentions |
partec flomax (RRID:SCR_014026) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values. | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014026 | 2026-08-13 09:29:07 | 7 | ||||||||||||
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HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | data analysis software, data processing software, software application, network analysis software, software resource | Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes. | Hetionet, matrix storage, operations on hetnets, hetnets, heterogeneous networks, | Gordon and Betty Moore Foundation ; NHGRI R01 HG010067; NCI R01 CA237170 |
PMID:36711546 | Free, Available for download, Freely available | SCR_023409 | hetmatpy | 2026-08-13 09:31:03 | 1 | ||||||||
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University of Chicago Digestive Diseases Research Core Center Resource Report Resource Website 1+ mentions |
University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) | DDRCC | data or information resource, organization portal, training resource, portal | Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis. | DDRCC, digestive disease, uchicago |
is listed by: NIDDK Information Network (dkNET) is parent organization of: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Administrative Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Administrative Core has organization facet: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is organization facet of: Digestive Disease Centers |
digestive disease | NIDDK P30 DK042086 | Available to the research community | SCR_015601 | 2026-08-13 09:29:24 | 1 | |||||||
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pillow Resource Report Resource Website 10+ mentions |
pillow (RRID:SCR_023337) | software toolkit, software resource, software library | Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool. | Python Imaging Library, image processing capabilities, foundation for general image processing, | Free, Available for download, Freely available | SCR_023337 | 2026-08-13 09:31:02 | 13 | |||||||||||
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mia Resource Report Resource Website 10+ mentions |
mia (RRID:SCR_023619) | data analysis software, data processing software, software resource, software application | Software R package with several tools for microbiome data analysis. | microbiome data, microbiome data analysis, | is related to: R Project for Statistical Computing | Free, Available for download, Freely available | https://github.com/microbiome/mia | SCR_023619 | 2026-08-13 09:30:48 | 10 | |||||||||
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Alfred Resource Report Resource Website 10+ mentions |
Alfred (RRID:SCR_023354) | web application, software resource, algorithm resource | Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas. | alignment, BAM, quality control, cell barcode splitting, annotation directed improvement, BAM alignment statistics, feature counting, feature annotation. | NHGRI U41HG007497 | PMID:30520945 | Free, Available for download, Freely available | https://bio.tools/alfred | SCR_023354 | 2026-08-13 09:31:02 | 18 | ||||||||
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BlobTools2 Resource Report Resource Website 100+ mentions |
BlobTools2 (RRID:SCR_023351) | data analysis software, data processing software, software resource, software application | Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier. | interactive quality assessment, genome assemblies, identifying and isolating non-target data, genome, QC, filtering, process assembly, read and analysis files, |
is related to: Blobtools is related to: Blobtoolkit |
BBSRC Bioinformatics and Biological Resources fund | PMID:32071071 | Free, Available for download, Freely available | https://github.com/blobtoolkit/blobtoolkit | SCR_023351 | blobtoolkit | 2026-08-13 09:30:44 | 383 | ||||||
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BigSeqKit Resource Report Resource Website 1+ mentions |
BigSeqKit (RRID:SCR_023592) | software toolkit, software resource, software library | Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core. | FASTA file, Q file, file manipulation, process FASTA and FASTQ files, | Free, Available for download, Freely available | SCR_023592 | 2026-08-13 09:30:48 | 1 | |||||||||||
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TIGER Data Portal Resource Report Resource Website 10+ mentions |
TIGER Data Portal (RRID:SCR_023626) | topical portal, data or information resource, disease-related portal, portal | Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets. | Type 2 Diabetes, genetic and epigenetic, functional data, molecular data, clinical data, pancreatic beta cells. | is related to: T2DSystems | Type 2 Diabetes | European Union Horizon 2020 ; Spanish government ; Swiss State Secretariat for Education‚ Research and Innovation ; American Diabetes Association Innovative and Clinical Translational Award ; Research England ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545 |
PMID:34644572 | SCR_023626 | Translational Human Pancreatic Islet Genotype Tissue-Expression Resource | 2026-08-13 09:31:07 | 23 | |||||||
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X2K Web Resource Report Resource Website 10+ mentions |
X2K Web (RRID:SCR_023624) | X2K | data access protocol, software resource, web service | Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks. | predicts involvement of upstream cell signaling pathways, differentially expressed genes, linking expression signatures, upstream cell signaling networks, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIH Office of the Director OT3 OD025467 |
PMID:29800326 | Free, Freely available | https://github.com/MaayanLab/x2k_web | SCR_023624 | eXpression2Kinases (X2K) Web | 2026-08-13 09:31:07 | 25 | |||||
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UpSetPlot Resource Report Resource Website 1+ mentions |
UpSetPlot (RRID:SCR_023225) | data processing software, software resource, data visualization software, software application | Software Python implementation of UpSet plots to visualize set overlaps. | UpSet plots, Python, visualize set overlaps, | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_023225 | 2026-08-13 09:30:43 | 7 | |||||||||
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Diabetes Data and Hypothesis Hub Resource Report Resource Website 1+ mentions |
Diabetes Data and Hypothesis Hub (RRID:SCR_023629) | D2H2 | topical portal, data or information resource, disease-related portal, database, portal | Platform that facilitates data driven hypothesis generation for diabetes and related metabolic disorder research community. Curated transcriptomics datasets from various Type 2 Diabetes studies are made available for download, visualization, and enrichment analysis. | diabetes, metabolic disorder, diabetes related metabolic disorder, transcriptomics datasets, |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Type 2 Diabetes | Free, Freely available | SCR_023629 | Diabetes Data and Hypothesis Hub (D2H2) | 2026-08-13 09:30:48 | 2 | |||||||
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Korea Statistical Information Service Resource Report Resource Website 50+ mentions |
Korea Statistical Information Service (RRID:SCR_023565) | data or information resource, data access protocol, software resource, web service | Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD. | Korean statistics, public data, international finance and economy, | Free, Freely available | SCR_023565 | KOSIS | 2026-08-13 09:31:06 | 72 | ||||||||||
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Children's Hospital Association Pediatric Health Information System Resource Report Resource Website 1+ mentions |
Children's Hospital Association Pediatric Health Information System (RRID:SCR_023168) | PHIS | topical portal, data or information resource, database, portal | Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals. | Children's hospitals, PHIS database, pediatrics data, clinical and resource utilization data, inpatient data, ambulatory surgery data, emergency department data, observation unit data | Free, Freely available | SCR_023168 | Pediatric Health Information System | 2026-08-13 09:30:59 | 5 | |||||||||
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BLIMP: Biomedical LIterature Mining Publications Resource Report Resource Website 1+ mentions |
BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) | BLIMP | data or information resource, bibliography | Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication. | biomedical, literature, text mining, bibliography, journal, text, biomedicine, natural language processing, information extraction, information retrieval, text categorization, ontology | has parent organization: Queens University; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada ; Queen's University Principal's Development Award ; NSERC Discovery 298292-04 |
The community can contribute to this resource | nif-0000-21063 | SCR_007112 | Biomedical LIterature (and text) Mining Publications | 2026-08-13 09:27:44 | 1 |
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