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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | data processing software, software application, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-09-12 01:00:54 | 5 | |||||
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Rhesus Macaque Atlases for Functional and Structural Imaging Studies Resource Report Resource Website 10+ mentions |
Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) | Rhesus Macaque Atlases | atlas, data or information resource | NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL. | magnetic resonance imaging, macaca mulatta, neuroscience, rhesus macaque, structure, neuroimaging, t1-weighted atlas, t2-weighted atlas, mri, brain, neuroanatomy | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | Aging | Intramural Research Program ; NCRR RR000167; NIA AG11915; NIA AG20013; NIGMS GM007507; NCRR RR00163; NIA AG029612 |
PMID:19059346 | NO LONGER AVAILABLE | nif-0000-33003 | SCR_008650 | 2026-09-12 01:02:01 | 10 | |||||
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Knowledge Engineering from Experimental Design Resource Report Resource Website 1+ mentions |
Knowledge Engineering from Experimental Design (RRID:SCR_001238) | KEfED | software application, software resource | Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable. | experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, java |
is listed by: FORCE11 is related to: Bioscholar has parent organization: Biomedical Informatics Research Network |
NIGMS R01-GM083871; NIMH 1R01MH079068-01A2; NCRR 1 U24 RR025736-01 |
PMID:21859449 | Free, Available for download, Freely available | nif-0000-07745 | https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29 | SCR_001238 | 2026-09-12 01:02:26 | 1 | |||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-09-12 01:02:32 | 20 | ||||||
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NIGMS Inside Life Science Resource Report Resource Website |
NIGMS Inside Life Science (RRID:SCR_005852) | Inside Life Science | data or information resource, narrative resource | The NIGMS Inside Life Science series brings you inside the science of health. Each story shows how basic biomedical researchfrom the history of a field to the people doing cutting-edge work todaylays the foundation for advances in disease diagnosis, treatment and prevention. Through explorations of how the body works and highlights from recent studies, you''ll discover even more on what scientists have found and are finding about fundamental life processes. NIGMS supported all of the featured research. | science, health, biomedical research, disease, diagnosis, treatment, prevention | has parent organization: National Institute of General Medical Sciences | NIGMS | nlx_149383 | SCR_005852 | 2026-09-12 01:02:34 | 0 | ||||||||
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LONI MiND Resource Report Resource Website |
LONI MiND (RRID:SCR_004820) | MiND | service resource, software resource | The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework. | diffusion magnetic resonance imaging, metadata, dwi, dti, software interoperability, data sharing | has parent organization: David Geffen School of Medicine at UCLA; California; USA | NIH ; NCRR ; NIMH ; NCRR 1U54RR021813-01; NIGMS 5T32GM008042-25; NCRR P41 RR013642; NIMH R01 MH71940; NIBIB EB008432; NIBIB EB008281; NIBIB EB007813; NICHD HD050735 |
PMID:20206274 | nlx_143920 | http://mind.loni.ucla.edu/ | SCR_004820 | MiND: Metadata in NIfTI for DWI, Metadata in NIfTI for DWI | 2026-09-12 01:02:33 | 0 | |||||
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zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NHGRI HG006431; NIDA DA14546; NIGMS GM63904 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-09-12 01:02:36 | 4 | ||||
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eProbalign Resource Report Resource Website |
eProbalign (RRID:SCR_013247) | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. | multiple sequence alignments, partition function posterior probabilities, bio.tools |
uses: Probalign is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: New Jersey Institute of Technology; New Jersey; USA |
NIGMS R01 GM073082 | PMID:17485479 | OMICS_00975, biotools:eprobalign | https://bio.tools/eprobalign | SCR_013247 | eProbalign web server, EProbalign | 2026-09-12 01:02:10 | 0 | ||||||
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Glycosylation Pathways Database Resource Report Resource Website 500+ mentions |
Glycosylation Pathways Database (RRID:SCR_013486) | data or information resource, database | A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category | binding, carbohydrate, glycoenzyme, glycosylation, pathway, protein | NIGMS | nif-0000-20850 | SCR_013486 | GTDB | 2026-09-12 01:02:12 | 859 | |||||||||
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Brain RNA-Seq Resource Report Resource Website 100+ mentions |
Brain RNA-Seq (RRID:SCR_013736) | data or information resource, database | Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list | has parent organization: Stanford University; Stanford; California | NIGMS T32GM007365; NIMH R01MH09955501; NINDS R01NS08170301 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | Barres Brain RNA-Seq | 2026-09-12 01:02:13 | 156 | |||||
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HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | data or information resource, database | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NCI T32 CA009528; NHGRI R01 HG005998; NHGRI T32 HG003284; NHLBI U54 HL117798; NIGMS P20 GM103534; NIGMS P50 GM071508; NIGMS R01 GM071966; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-09-12 01:02:16 | 95 | ||||||||
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MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | data or information resource, database | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Charles E. Culpeper Scholarship in Medical Science ; Howard Hughes Medical Institute ; NIDDK DK43351; NIDDK DK57521; NIGMS GM0077465 |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-09-12 01:02:18 | 208 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI CA295532; NIGMS ; NIH |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-09-12 01:02:17 | 1702 | ||||||
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NETMAGE Resource Report Resource Website 1+ mentions |
NETMAGE (RRID:SCR_021843) | 2d spatial image, data or information resource, image | Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes. | PheWAS, genetic associations from Phenome Wide Association Study, disease-disease network construction, phenotypes, shared genetic associations between phenotypes | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIGMS | DOI:10.1101/2020.10.27.357103 | Free, Available for download, Freely available | SCR_021851 | https://github.com/dokyoonkimlab/netmage | SCR_021843 | 2026-09-12 01:02:20 | 2 | ||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | 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 | 2026-09-12 01:01:04 | 15 | ||||||
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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 | 2026-09-12 01:01:05 | 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 | 2026-09-12 01:01:04 | 39 | ||||||
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mosdepth Resource Report Resource Website 50+ 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 |
NCI U24 CA209999; NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-09-12 01:01:08 | 56 | ||||||
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ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | data or information resource, portal, project 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 |
Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; European Research Council ; German Federal Ministry of Education and Research ; NCRR S10 RR027584; NHGRI RC2 HG005805; NIGMS P50 GM076547; NIGMS R01 GM087221; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-09-12 01:01:07 | 23 | |||||||
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GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | data or information resource, portal, project 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 | 2026-09-12 01:01:12 | 20 |
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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 U24DK097771.
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