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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
iBioSeminars
 
Resource Report
Resource Website
iBioSeminars (RRID:SCR_005848) iBioSeminars training material, narrative resource, data or information resource, video resource iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB. biological research, biology, lecture, seminar, education, undergraduate, graduate has parent organization: University of California at San Francisco; California; USA
has parent organization: American Society for Cell Biology
has parent organization: Howard Hughes Medical Institute
NSF ;
NIGMS ;
Howard Hughes Medical Institute
Licensed under a Creative Commons Attribution-NonCommercial-NoDerivs v3 Unported License. nlx_149380 SCR_005848 iBioSeminars - Bringing the World''s Best Biology to You, iBioSeminars - Bringing the Worlds Best Biology to You, iBioSeminars.org 2026-02-16 09:46:41 0
PhysioNet
 
Resource Report
Resource Website
500+ mentions
PhysioNet (RRID:SCR_007345) PhysioNet data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material. physiologic, physiology, signal, software, research, biomedical, cardiopulmonary, neural, healthy, patient, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, cardioogy, computation, physiologic signal, workspace, time series, FASEB list is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: DataCite
is listed by: re3data.org
is listed by: FAIRsharing
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
is parent organization of: CHB-MIT Scalp EEG Database
is parent organization of: EEG Motor Movement/Imagery Dataset
is parent organization of: Sleep-EDF Database
Aging NIBIB ;
NIGMS
PMID:22256277
PMID:14716615
PMID:14632011
PMID:11446213
PMID:10851218
Free, Freely available r3d100011561, nif-0000-00250, DOI:10.17616/R3D06S, DOI:10.25504/FAIRsharing.bemzxg, DOI:10.13026 https://doi.org/10.17616/R3D06S
https://doi.org/10.17616/r3d06s
https://doi.org/10.13026/
https://dx.doi.org/10.13026/
https://fairsharing.org/10.25504/FAIRsharing.bemzxg
https://doi.org/10.17616/R3D06S
SCR_007345 Physionet: The Research Resource for Complex Physiologic Signals, PhysioNet, PhysioNet: The Research Resource for Complex Physiologic Signals 2026-02-16 09:46:57 618
Molecular Dynamics Workflow (BioKepler)
 
Resource Report
Resource Website
1+ mentions
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) data processing software, software application, software resource, workflow software A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. workflow, MD, molecular dynamics, simulation, software, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: bioKepler
has parent organization: University of California at San Diego; California; USA
NIGMS P41GM103426 Requires Linux biotools:ambergpumdsimulation http://nbcr.ucsd.edu/data/downloads/workflows/
https://bio.tools/ambergpumdsimulation
SCR_014389 Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation 2026-02-16 09:48:38 1
WikiPathways
 
Resource Report
Resource Website
1000+ mentions
WikiPathways (RRID:SCR_002134) service resource, data or information resource, database Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list is used by: NIF Data Federation
is used by: Open PHACTS
is related to: PharmGKB
is related to: Reactome
is related to: NetPath
is related to: ConsensusPathDB
is related to: NCBI BioSystems Database
is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit
has parent organization: University of California at San Francisco; California; USA
has parent organization: Maastricht University; Maastricht; Netherlands
NIH ;
Netherlands Bioinformatics Centre ;
Google Summer of Code program ;
NWO - Netherlands Organization for Scientific Research ;
NIGMS GM080223;
NIGMS R01 GM100039
PMID:22096230
PMID:18651794
Free, Freely available nif-0000-20925 SCR_002134 Wiki Pathways 2026-02-16 09:45:40 1696
bioPIXIE
 
Resource Report
Resource Website
1+ mentions
bioPIXIE (RRID:SCR_004182) bioPIXIE production service resource, service resource, data analysis service, analysis service resource bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). prediction, bayesian network, probabilistic, interaction, network has parent organization: Princeton University; New Jersey; USA NHGRI T32 HG003284;
NIGMS R01 GM071966;
NHGRI R01 HG003471;
NIGMS P50 GM071508;
NSF DGE-9972930;
NSF IIS-0513552
PMID:16420673 nlx_20893 SCR_004182 biological Process Inference from eXperimental Interaction Evidence 2026-02-16 09:46:17 1
Zebrafinch Brain Architecture Project
 
Resource Report
Resource Website
1+ mentions
Zebrafinch Brain Architecture Project (RRID:SCR_004277) Zebrafinch Brain Architecture Project data or information resource, atlas Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies. nissl stain, sagittal, horizontal plane, transverse plane, myelin stain, brain has parent organization: Brain Architecture Project W. M. Keck Foundation ;
Crick-Clay Professorship ;
NINDS NS50436;
NIGMS R24 GM092842
nlx_143663 SCR_004277 2026-02-16 09:46:15 5
ProFunc
 
Resource Report
Resource Website
50+ mentions
ProFunc (RRID:SCR_004450) ProFunc production service resource, service resource, data analysis service, analysis service resource The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time. gold standard is related to: PDBsum
has parent organization: European Bioinformatics Institute
DOE contract W-31-109-Eng-38;
NIGMS GM62414;
European Union FP6 contract LHSG-CT-2003-503265
PMID:15980588
PMID:16019027
nlx_44430 SCR_004450 ProFunc - prediction of protein function from 3D structure, ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function 2026-02-16 09:46:22 63
ADMIXTOOLS
 
Resource Report
Resource Website
100+ mentions
ADMIXTOOLS (RRID:SCR_018495) software resource, software toolkit Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Harvard University; Cambridge; United States
U.S. National Science Foundation HOMINID ;
NIGMS GM100233
PMID:22960212 Free, Available for download, Freely available biotools:admixtools http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html.
https://bio.tools/admixtools
SCR_018495 2026-02-16 09:49:28 205
FluCalc
 
Resource Report
Resource Website
1+ mentions
FluCalc (RRID:SCR_019322) software application, software resource, data analytics software Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis. Estimator, fluctuation calculation, MSS-MLE, Ma-Sandri-Sarkar Maximum Likelihood Estimator, calculator, fluctuation analysis has parent organization: Tufts University; Massachusetts; USA NIGMS GM105473;
NIGMS GM60987
PMID:29043640 Free, Available for download, Freely available SCR_019322 flucalc, fluctuation calculation 2026-02-16 09:49:43 1
CellChat
 
Resource Report
Resource Website
500+ mentions
CellChat (RRID:SCR_021946) software resource, software toolkit Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data NSF DMS1763272;
Simons Foundation ;
NIH U01 AR073159;
NIGMS R01 GM123731;
NIH P30 AR07504;
Pew Charitable Trust ;
LEO Foundation ;
UC Irvine ;
Howard Hughes Medical Institute
PMID:33597522 Free, Available for download, Freely available http://www.cellchat.org/ SCR_021946 2026-02-16 09:50:10 536
SYGNAL
 
Resource Report
Resource Website
1+ mentions
SYGNAL (RRID:SCR_023080) software resource, software toolkit Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, NIGMS P50GM076547;
NIGMS R01GM077398;
NSF ABI NSF-1262637;
NSF DBI-0640950;
NCI U24CA143835;
American Cancer Society Research Scholar Grant
PMID:27426982 Free, Available for download, Freely available SCR_023080 SYstems Genetic Network AnaLysis 2026-02-16 09:50:37 1
AmpliconArchitect
 
Resource Report
Resource Website
10+ mentions
AmpliconArchitect (RRID:SCR_023150) software resource, software toolkit Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon NIGMS R01GM114362;
NHGRI HG010149;
NSF NSF-DBI-1458557
DOI:10.1038/s41467-018-08200-y SCR_023150 2026-02-16 09:50:35 42
CarbonylDB
 
Resource Report
Resource Website
1+ mentions
CarbonylDB (RRID:SCR_023924) database, data or information resource Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools. Curated data, protein carbonylation site, chemically diverse form, irreversible oxidative post translational modifications, NIGMS R01 GM100701;
Danish Council for Independent Research–Technology and Production Sciences
PMID:29509874 Free, Available for download, Freely available SCR_023924 2026-02-16 09:50:36 1
National Magnetic Resonance Facility at Madison
 
Resource Report
Resource Website
1+ mentions
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) NMRFAM service resource, access service resource, training resource Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center has parent organization: University of Wisconsin-Madison; Wisconsin; USA NIGMS R24GM141526;
NIGMS P41136463
Free, Freely Available nlx_152672 SCR_001449 2026-02-16 09:45:29 4
Laboratory for Fluorescence Dynamics
 
Resource Report
Resource Website
10+ mentions
Laboratory for Fluorescence Dynamics (RRID:SCR_001437) LFD service resource, access service resource, biomedical technology research center, training resource Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community. fluorescence, measurement, microscopy, spectroscopy, biochemistry, cell culture, data analysis, biomolecule, membrane, in-vitro, optical spectroscopy, biological process, tissue culture, fluorescence microscopy, optical and laser technology center has parent organization: University of California at Irvine; California; USA NIGMS 8P41GM103540;
NCRR 5P41RR003155
Restricted nlx_152663 SCR_001437 Laboratory for Fluorescence Dynamics (LFD) 2026-02-16 09:45:29 47
BioCARS
 
Resource Report
Resource Website
50+ mentions
BioCARS (RRID:SCR_001439) BioCARS service resource, access service resource, biomedical technology research center, training resource Biomedical technology research center and training resource that is a state-of-the art, national user facility for synchrotron-based studies of dynamic and static properties of macromolecules by X-ray scattering techniques such as crystallography (specializing in time-resolved), small- and wide-angle X-ray scattering and fiber diffraction. BioCARS operates two X-ray beamlines, embedded in a Biosafety Level 3 (BSL-3) facility unique in the U.S. that permits safe studies of biohazardous materials such as human pathogens., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. synchrotron, macromolecule, x-ray, crystallography, x-ray scattering, fiber diffraction, biological process, time-resolved crystallography, structural biology technology center has parent organization: University of Chicago; Illinois; USA NIGMS P41GM103543;
NCRR P41RR007707
PMID:21685684 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152665 http://cars9.uchicago.edu/biocars/ SCR_001439 BioCARS: A Synchrotron Structural Biology Resource 2026-02-16 09:45:29 64
miRanda
 
Resource Report
Resource Website
100+ mentions
miRanda (RRID:SCR_017496) service resource, data or information resource, database Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list is listed by: SoftCite NIGMS ;
Atlantic Philanthropies ;
Alfred W. Bressler Scholars Endowment Fund
PMID:18158296 THIS RESOURCE IS NO LONGER IN SERVICE http://www.microrna.org/microrna/home.do SCR_017496 MicroRNA.org. microrna.org 2026-02-16 09:49:15 210
CIS-BP
 
Resource Report
Resource Website
100+ mentions
CIS-BP (RRID:SCR_017236) web service, data access protocol, database, software resource, data or information resource Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs. catalog, inferred, sequence, binding, preference, transcription, factor, DNA, motif, FASEB list Canadian Institutes of Health Research ;
Canadian Institute for Advanced Research Junior Fellows Genetic Networks Program ;
NICHD P01 HD39691;
NIGMS GM082971;
EU Marie Curie International Outgoing Fellowship ;
NSF MCB-1024999;
Howard Hughes Medical Institute ;
Gordon and Betty Moore Foundation ;
Millennium Nucleus for Fungal Integrative and Synthetic Biology ;
Fondo Nacional de Desarrollo Científico y Tecnológico
PMID:25215497 Free, Freely available r3d100013971 https://doi.org/10.17616/R31NJN9V SCR_017236 Catalog of Inferred Sequence Binding Preferences 2026-02-16 09:49:11 104
SRMAtlas
 
Resource Report
Resource Website
1+ mentions
SRMAtlas (RRID:SCR_016996) SRM Atlas, SRMatlas data or information resource, database, atlas Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide American Recovery and Reinvestment Act ;
NHGRI RC2 HG005805;
NIGMS R01 GM087221;
NCRR S10 RR027584;
NIGMS P50 GM076547;
Luxembourg Centre for Systems Biomedicine University Luxembourg ;
European Research Council ;
Swiss National Science Foundation
PMID:27453469 Publicly available, Registration required SCR_016996 2026-02-16 09:49:08 3
Integrative Modeling Platform
 
Resource Report
Resource Website
50+ mentions
Integrative Modeling Platform (RRID:SCR_002982) IMP software resource, software toolkit An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. Its broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. It can also be used from the Chimera molecular modeling system, or via one of several web applications. integrative modeling, structure determination, hybrid modeling, macromolecular assembly, c++, python, peptide, biomolecule, model, structural characterization, structure is related to: UCSF Chimera
has parent organization: University of California at San Francisco; California; USA
NIGMS R01 GM083960 PMID:22272186 GNU Lesser General Public License, v2.1 or later, Acknowledgement requested, GNU General Public License SciRes_000187 SCR_002982 IMP - the Integrative Modeling Platform, Integrative Modeling Platform (IMP), IMP the Integrative Modeling Platform 2026-02-16 09:45:58 54

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