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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | software application, software resource, data analysis software, data processing software | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NHLBI U54 HL127624; NCI U54 CA189201; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | GENE Expression and Enrichment Vector Analyzer | 2026-07-28 09:44:07 | 5 | |||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | software application, web application, data or information resource, database, software resource, data processing software, data visualization software | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-07-28 09:43:55 | 3 | |||||||
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | database, data or information resource, web application, software resource | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-07-28 09:43:56 | 24 | |||||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | software application, simulation software, software toolkit, software resource | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NSF Graduate Research Fellowship ; Simons Foundation ; NIGMS GM078221; NIGMS GM73141; NIGMS GM114961; NIGMS GM084453; NIGMS GM111819; NSF BMAT 1507736; NCI F32 CA189246; NIGMS GM092802; NIGMS GM110089; NIGMS GM117189 |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-07-28 09:43:59 | 212 | |||||||
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fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | software application, algorithm resource, software resource, data processing software, alignment software, standalone software, image analysis software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-07-28 09:44:05 | 4 | |||||||
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Glam2 Resource Report Resource Website 50+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-07-28 09:44:09 | 72 | |||||
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Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | software application, source code, software resource, data processing software, data visualization software | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
the Alfred P. Sloan Foundation ; NIGMS GM083107; NIGMS GM084222; NSF 0746198 |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-07-28 09:44:13 | 4 | |||||
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Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | software application, web application, data or information resource, database, software resource, data processing software, data visualization software | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NIGMS R01 GM098316; NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-07-28 09:44:11 | 127 | |||||||||
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lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373; NICHD R01 HD084633 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-07-28 09:44:12 | 3 | |||||||
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APA-Scan Resource Report Resource Website |
APA-Scan (RRID:SCR_022974) | software application, data analysis software, software resource, data processing software, data visualization software | Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data. | annotated and potential alternative polyadenylation events, gene downstream 3'-UTR, RNA-seq and 3'-end-seq data, two different biological conditions, polyadenylation events | NSF FET2003749; NIGMS R01GM113952; NIDDK DK097771 |
PMID:36171568 | Free, Available for download, Freely available | SCR_022974 | 2026-07-28 09:45:45 | 0 | |||||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | software resource, data access protocol, 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 | 2026-07-28 09:45:57 | 24 | |||||||
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MicrobeJ Resource Report Resource Website 1+ mentions |
MicrobeJ (RRID:SCR_023914) | software application, data analysis software, software resource, data processing software, image processing software | 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 | 2026-07-28 09:46:01 | 6 | ||||||||
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Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | software resource, data access protocol, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-07-28 09:45:58 | 11 | |||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | software resource, data access protocol, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-07-28 09:46:09 | 6 | ||||||||
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HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism Resource Report Resource Website 50+ mentions |
HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) | HumanCyc | service resource, data or information resource, data analysis service, database, software resource, production service resource, analysis service resource | The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version. | enzyme, function, functional, gene, genome, genomic, human, human genome, metabolic, metabolism, mitochondrion, nucleotide, pathway, position, reaction, sequence, metabolomics, gene expression, bioreaction, metabolic pathway, nutrition, FASEB list |
is listed by: BioCyc is related to: Pathway Commons is related to: ConsensusPathDB is related to: BioCyc is related to: Pathway Tools has parent organization: Stanford Research Institute International |
Pharmaceutical company ; NIGMS GM092729 |
PMID:15642094 | Public | r3d100011286, nif-0000-21206 | https://doi.org/10.17616/R3ZS72 | SCR_007050 | 2026-07-28 09:41:43 | 60 | |||||
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microRNA.org Resource Report Resource Website 1000+ mentions |
microRNA.org (RRID:SCR_006997) | microRNA.org | data or information resource, database, software resource | Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microrna, gene, expression, gene regulation, FASEB list |
is listed by: OMICtools is listed by: SoftCite |
NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03127, OMICS_00402 | SCR_006997 | microRNA.org - Targets and Expression | 2026-07-28 09:41:40 | 2648 | |||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | service resource, data or information resource, data repository, catalog, database, storage service resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-07-28 09:41:46 | 39 | ||||
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Rankprop - Protein Ranking by Network Propagation Resource Report Resource Website |
Rankprop - Protein Ranking by Network Propagation (RRID:SCR_007159) | service resource, source code, data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on May,18,2020. Ranking algorithm that exploits global network structure of similarity relationships among proteins in database by performing diffusion operation on protein similarity network with weighted edges. Source code and web server for searching non-redundant protein database. Web server ranks proteins found in NRDB40 (from PairsDB) against query sequence of amino acids using Rankprop algorithm. | Ranking algorithm, network structure, protein database, similarity relationship, protein similarity network, weighted adges, non redundat protein database, protein database search | has parent organization: University of Washington; Seattle; USA | NSF EIA-0312706; NSF DBI-0243257; NIGMS GM74257 |
PMID:16723003 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_50351 | http://rankprop.gs.washington.edu/info.php | SCR_007159 | Rankprop | 2026-07-28 09:41:44 | 0 | |||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | data or information resource, topical portal, portal | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-07-28 09:41:57 | 2 | |||||
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Yeast snoRNA Database Resource Report Resource Website 1+ mentions |
Yeast snoRNA Database (RRID:SCR_007980) | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms. | saccharomyces cerevisiae |
is related to: 3D Ribosomal Modification Maps Database has parent organization: University of Massachusetts Amherst; Massachusetts; USA |
U.S. Public Health Service ; NIGMS GM19351 |
PMID:17283215 | nif-0000-03651 | http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | SCR_007980 | Yeast snoRNA Database at UMass-Amherst | 2026-07-28 09:42:00 | 1 |
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