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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CWL-Airflow Resource Report Resource Website 1+ mentions |
CWL-Airflow (RRID:SCR_017196) | CWL DAG | data processing software, software application, software resource, workflow software | Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms. | airflow, common workflow language, cwl, pipeline, workflow, docker | is listed by: OMICtools | NCATS UL1 TR001425; NIGMS DP2 GM119134 |
DOI:10.1101/249243 DOI:10.1093/gigascience/giz084 |
Free, Available for download, Freely available | OMICS_26560 | SCR_017196 | CWL-Airflow v 1.0.16, Common Workflow Language-Airflow | 2026-02-16 09:49:11 | 2 | |||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-02-16 09:49:13 | 7 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | software application, data processing software, image processing software, image analysis software, software resource | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-02-16 09:49:14 | 1 | |||||||
|
FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Weizmann Institute Advancing Women in Science ; NIGMS R01 GM083960; NCRR U54 RR022220; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Lawrence Berkeley National Lab IDAT program ; NIGMS P41 GM109824 |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-02-16 09:49:12 | 20 | |||||||
|
BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
Royal Society of New Zealand Marsden award ; European Research Council ; NIGMS U01 GM110749; Swiss National Science foundation ; Max Planck Society ; EMBL |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-02-16 09:49:12 | 194 | |||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-02-16 09:49:16 | 4 | ||||||
|
Modeling Infectious Disease Agents Study online portal for COVID-19 Resource Report Resource Website 1+ mentions |
Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) | data or information resource, topical portal, portal | Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases. | COVID-19, COVID-19 data, modeling research, public data, metadata, infectious disease | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | NIGMS | Free, Freely available | https://github.com/midas-network/COVID-19 | SCR_018281 | MIDAS online portal for COVID-19 | 2026-02-16 09:49:26 | 4 | ||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | data processing software, software application, software resource | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth https://sources.debian.org/src/mosdepth/ |
SCR_018929 | 2026-02-16 09:49:34 | 38 | ||||||
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GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | data or information resource, project portal, portal | Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression. | Gly-glycobiology Gen-information, glycobiology, glycans molecular properties, glycans biophysical properties, glycans functional properties properties, glycans, genes, proteins, lipids, pathways and ontologies, data, mutation and expression data, carbohydrate and glycoconjugate related data, | NIGMS 1U01GM125267; NIGMS R24 GM146616 |
PMID:31616925 PMID:32324859 |
Free, Freely available | SCR_023438 | GlyGen Portal | 2026-02-16 09:50:36 | 11 | ||||||||
|
Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, database, project portal, portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-02-16 09:50:45 | 55 | |||||||
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WTCHG Genome Scan Viewer Resource Report Resource Website 1+ mentions |
WTCHG Genome Scan Viewer (RRID:SCR_001635) | GSCANDB | service resource, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. | genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression | has parent organization: University of Oxford; Oxford; United Kingdom | NIAAA U01AA014425; NCRR R24RR015116; NIGMS R01GM072863; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153902 | SCR_001635 | Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database | 2026-02-16 09:45:32 | 3 | ||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | service resource, data or information resource, database | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-02-16 09:46:02 | 0 | ||||||
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CellProfiler Image Analysis Software Resource Report Resource Website 1000+ mentions |
CellProfiler Image Analysis Software (RRID:SCR_007358) | data processing software, software application, software resource, image analysis software | Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types. | high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithm |
is listed by: Debian is related to: CellProfiler Analyst has parent organization: Broad Institute |
NIGMS R01 GM089652; NIGMS RC2 GM092519; NHGRI RL1 HG004671 |
PMID:21349861 PMID:17076895 PMID:19014601 PMID:19188593 |
Free, Available for download, Freely available | SCR_010649, nlx_66812, nif-0000-00280 | https://sources.debian.org/src/cellprofiler/ | SCR_007358 | Cell Profiler, CellProfiler - cell image analysis software | 2026-02-16 09:46:57 | 3265 | |||||
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Ontodog: A Web-based Ontology View Generator Resource Report Resource Website 10+ mentions |
Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) | Ontodog | production service resource, service resource, source code, software resource | Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0. | ontology, interoperability | has parent organization: University of Michigan Medical School; Michigan; USA | Rackham Pilot Research ; NIAID R01AI081062; NIGMS 5R01GM93132-1 |
nlx_144053 | SCR_005061 | 2026-02-16 09:46:26 | 17 | ||||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, software application, software resource, image analysis software | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-02-16 09:49:00 | 13 | ||||||
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RSRef Resource Report Resource Website 1+ mentions |
RSRef (RRID:SCR_017211) | data processing software, software application, software resource | Software for fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy. | Fitting, atomic, model, density, map, x ray, crystallography, electron, microscopy | NIGMS R01 GM66875; NIGMS R01 GM78538 |
PMID:23376441 | Free, Available for download, Freely available | http://xtal.ohsu.edu/software/rsref/readme.txt | SCR_017211 | 2026-02-16 09:49:11 | 1 | ||||||||
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-02-16 09:49:05 | 39 | ||||||
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ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | data or information resource, project portal, portal | Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research. | Molecular tool, human proteome, proteome, human, peptide, data |
is related to: ProteomicsDB is related to: ProteomeXchange |
German Federal Ministry of Education and Research ; Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; NHGRI RC2 HG005805; NIGMS R01 GM087221; NCRR S10 RR027584; NIGMS P50 GM076547; European Research Council ; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-02-16 09:49:31 | 21 | |||||||
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MicrobeJ Resource Report Resource Website 1+ mentions |
MicrobeJ (RRID:SCR_023914) | software application, data processing software, data analysis software, image processing software, software resource | Software tool for high throughput bacterial cell detection and quantitative analysis. Used to analyze bacterial cells. Used to process images derived from variety of microscopy experiments with special emphasis on large image sets. Performs intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. | bacterial cell detection, analyze bacterial cells, bacteria quantitative analysis, process images, intensity and morphology measurements, | is a plug in for: ImageJ | NIGMS GM51986; NIGMS GM113172; Indiana University Office of the Vice President for Research ; NCATS UL1TR001108 |
PMID:27572972 | Free, Available for download, Freely available | SCR_023914 | 2026-02-16 09:50:43 | 6 | ||||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | NIGMS 5T32GM080177; NCI 1R33CA212697; Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/ https://github.com/AllonKleinLab/SPRING_dev |
SCR_023578 | 2026-02-16 09:50:48 | 24 |
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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 2U24DK097771-09.
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