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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
ChromHMM
 
Resource Report
Resource Website
10+ mentions
ChromHMM (RRID:SCR_018141) software application, software resource, data analysis software, data processing software Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern is listed by: Debian
is listed by: OMICtools
NHGRI U54 HG004570;
NHGRI RC1HG005334;
NIEHS R01 ES024995;
NHGRI U01 HG007912;
NIMH U01 MH105578;
NSF 0905968;
Alfred P. Sloan Fellowship ;
CAREER Award
PMID:29120462
PMID:22373907
Free, Available for download, Freely available OMICS_03490 https://sources.debian.org/src/chromhmm/ SCR_018141 2026-07-28 09:44:41 47
gProfiler2
 
Resource Report
Resource Website
50+ mentions
gProfiler2 (RRID:SCR_018190) software application, software resource, data analysis software, data processing software Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. Gene list, functional enrichment analysis, namespace conversion, data, analysis is listed by: ELIXIR Tools and Data Services Registry
is related to: R Project for Statistical Computing
works with: g:Profiler
Estonian Research Council grants ;
European Regional Development Fund for CoE of Estonian ICT research EXCITE projects
PMID:31066453 Free, Available for download, Freely available SCR_018190 gprofiler2 2026-07-28 09:44:51 53
QuB
 
Resource Report
Resource Website
1+ mentions
QuB (RRID:SCR_018076) QuB software application, data analysis software, software resource, data processing software, software toolkit Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis THIS RESOURCE IS NO LONGER IN SERVICE SCR_018076 Quantify unknown Biophysics 2026-07-28 09:44:49 2
MOON
 
Resource Report
Resource Website
1+ mentions
MOON (RRID:SCR_018005) software application, data analysis software, software resource, data processing software, software toolkit Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid Restricted SCR_018005 2026-07-28 09:44:48 6
UltraScan
 
Resource Report
Resource Website
10+ mentions
UltraScan (RRID:SCR_018126) software application, software resource, data analysis software, data processing software Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis NSF DBI 9724273;
NSF DBI 9974819;
NSF ANI 228927;
NSF TG-MCB 060019T;
NSF TG-MCB 070038;
NSF TG-MCB 070039;
NSF TG-MCB 070040;
NSF OCI 1032742;
NSF ACI 1339649;
NCRR RR022200;
NCRR RR 022200 03S1;
NIGMS GM120600;
San Antonio Life Science Institute ;
Howard Hughes Medical Institute ;
Robert J. Kleberg Jr. and Helen C. Kleberg Foundation
Free, Available for download, Freely available SCR_018126 2026-07-28 09:44:41 20
Gene Expression Profiling Interactive Analysis
 
Resource Report
Resource Website
5000+ mentions
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) GEPIA service resource, data access protocol, software resource, production service resource, web service, analysis service resource Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis. Cancer gene expression, normal gene expression, analysis, RNA sequencing, expression data, TCGA project, GTEx project, patient survival analysis, correlation analysis is related to: Gene Expression Profiling Interactive Analysis 2
has parent organization: Peking University; Beijing; China
Cancer Peking University ;
National Natural Science Foundation of China
PMID:28407145 Free, Freely available SCR_018294 2026-07-28 09:44:39 5635
SEDFIT
 
Resource Report
Resource Website
10+ mentions
SEDFIT (RRID:SCR_018365) software application, software resource, data analysis software, data processing software Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering is listed by: SoftCite NIH Free, Available for download, Freely available SCR_018365 SEDFIT version 14.7g 2026-07-28 09:44:44 25
piNET
 
Resource Report
Resource Website
1+ mentions
piNET (RRID:SCR_018693) service resource, data access protocol, software resource, production service resource, web service, analysis service resource Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data is related to: LINCS Project NHLBI U54 HL127624;
NIEHS P30 ES006096;
NIMH R01 MH107487;
NCI T32 CA236764;
NCATS UL1 TR001425;
NIGMS U01 GM120953
DOI:10.1093/nar/gkaa436 Free, Freely available SCR_018693 2026-07-28 09:44:48 4
TIMER
 
Resource Report
Resource Website
1000+ mentions
TIMER (RRID:SCR_018737) TIMER service resource, data access protocol, software resource, production service resource, web service, analysis service resource Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display National Natural Science Foundation of China ;
NCI CA180980;
Dana-Farber Cancer Institute
PMID:29092952 Free, Freely available SCR_018737 Tumor IMmune Estimation Resource 2026-07-28 09:44:48 2042
rVista
 
Resource Report
Resource Website
10+ mentions
rVista (RRID:SCR_018707) service resource, data access protocol, software resource, production service resource, web service, analysis service resource Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools is listed by: Debian
is listed by: bio.tools
works with: TRANSFAC
PMID:15215384 Free, Freely available biotools:rvista https://bio.tools/rvista SCR_018707 rVista 2.0 2026-07-28 09:44:44 30
EpiModel
 
Resource Report
Resource Website
1+ mentions
EpiModel (RRID:SCR_018539) software application, data analysis software, software resource, data processing software, software toolkit Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools is listed by: Debian
is listed by: bio.tools
NICHD R01 HD068395;
NIMH R21 MH112449;
NICHD R21 HD075662;
NIDA P30 DA027828;
NIAID P30 AI050409;
NIAID P30 AI027757;
NICHD T32 HD007543
PMID:29731699 Free, Available for download, Freely available biotools:epimodel https://bio.tools/epimodel SCR_018539 2026-07-28 09:44:46 7
QoRTs
 
Resource Report
Resource Website
10+ mentions
QoRTs (RRID:SCR_018665) software application, data analysis software, software resource, data processing software, software toolkit Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, NHGRI PMID:26187896 Free, Freely available https://github.com/hartleys/QoRTs SCR_018665 2026-07-28 09:44:47 26
GOnet
 
Resource Report
Resource Website
1+ mentions
GOnet (RRID:SCR_018977) service resource, software resource, data access protocol, web service Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
works with: Gene Ontology
NIH Common Fund ;
NIGMS ;
NHGRI R24 HG010032;
NIAID U19 AI118610;
NIAID U19 AI118626
PMID:30526489 biotools:GOnet https://github.com/mikpom/gonet, https://bio.tools/GOnet SCR_018977 2026-07-28 09:45:02 3
GeneNetWorks
 
Resource Report
Resource Website
1+ mentions
GeneNetWorks (RRID:SCR_008034) software application, data analysis software, data or information resource, database, software resource, data processing software, data visualization software, data acquisition software GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses. experimental, expression, gene, gene regulation, genetic, analysis, data, dna, graphical, molecular, navigation, network, program, protein, rna, software, system nif-0000-10232 SCR_008034 GNW 2026-07-28 09:41:58 1
Genomatix Software: Understanding Gene Regulation
 
Resource Report
Resource Website
500+ mentions
Genomatix Software: Understanding Gene Regulation (RRID:SCR_008036) software application, narrative resource, data analysis software, data or information resource, database, software resource, data processing software, short course material, topical portal, portal, training material THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 13,2026. Genomatix is a privately held company that offers software, databases, and services aimed at understanding gene regulation at the molecular level representing a central part of systems biology. Its multilayer integrative approach is a working implementation of systems biology principles. Genomatix combines sequence analysis, functional promoter analysis, proprietary genome annotation, promoter sequence databases, comparative genomics, scientific literature data mining, pathway databases, biological network databases, pathway analysis, network analysis, and expression profiling into working solutions and pipelines. It also enables better understanding of biological mechanisms under different conditions and stimuli in the biological context of your data. Some of Genomatix'' most valuable assets are the strong scientific background and the years of experience in research & discovery as well as in development & application of scientific software. Their firsthand knowledge of all the complexities involved in the in-silico analysis of biological data makes them a first-rate partner for all scientific projects involving the evaluation of gene regulatory mechanisms. The Genomatix team has more than a decade of scientific expertise in the successful application of computer aided analysis of gene regulatory networks, which is reflected by more than 150 peer reviewed scientific publications from Genomatix'' scientists More than 35,000 researchers in industry and academia around the world use this technology. The software available in Genomatix are: - GenomatixSuite: GenomatixSuite is our comprehensive software bundle including ElDorado, Gene2Promoter, GEMS Launcher, MatInspector and MatBase. GenomatixSuite PE also includes BiblioSphere Pathway Edition. Chromatin IP Software - RegionMiner: Fast, extensive analysis of genomic regions. - ChipInspector: Discover the real power of your microarray data. Genome Annotation Software - ElDorado: Extended Genome Annotation. - Gene2Promoter: Retrieve & analyze promoters - GPD: The Genomatix Promoter Database, which is now included with Gene2Promoter. Knowledge Mining Software - BiblioSpere : The next level of pathway/genomics analysis. - LitInspector: Literature and pathway analysis for free. Sequence Analysis Software - GEMS Launcher: Our integrated collection of sequence analysis tools. - MalInspector: Search transcription factor binding sites - MatBase: The transcription factor knowledge base. Other (no registration required) Software - DiAlign: Multiple alignment of DNA/protein sequence. - Genomatix tools: Various small tools for sequence statistics, extraction, formatting, etc. effect, expression, functional, gene, genome, alignment, analysis, annotation, biological, cascade, cell, data, dna, in-silico analysis, mechanism, metabolic pathway, microarray, mining, molecular, network, pathway, promoter, protein, region, regulation, scientific, sequence, signaling, software, stimulus, systems biology, technology, text mining, transcription, FASEB list has parent organization: Genomatix Solutions THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10236 http://www.genomatix.de/products/index.html SCR_008036 Genomatix 2026-07-28 09:42:16 868
GeneWindow
 
Resource Report
Resource Website
1+ mentions
GeneWindow (RRID:SCR_008183) software application, software resource, data analysis software, data processing software Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set is listed by: 3DVC
has parent organization: National Cancer Institute
nif-0000-21173 SCR_008183 GeneWindow 2026-07-28 09:42:04 1
FSL
 
Resource Report
Resource Website
1000+ mentions
FSL (RRID:SCR_002823) software library, software toolkit, software resource Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation uses: Neuroimaging Data Model
is used by: Spinal Cord Toolbox
is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND)
is used by: XFSL: An FSL toolbox
is used by: CMIND PY
lists: SUSAN
lists: FUGUE
lists: Miscvis
lists: BayCEST
lists: ICA-PNM
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: SoftCite
is related to: Rodent Brain Extraction Tool
is related to: Human Connectome Coordination Facility
is related to: BASH4RfMRI
is related to: DW-MRI registration in FSL
is related to: FSL extensions
is related to: Diffusion MRI of Traumatic Brain Injury
is related to: Segmentation of Hippocampus Subfields
is related to: masked ICA (mICA) Toolbox
has parent organization: University of Oxford; Oxford; United Kingdom
has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components
has plug in: FMRI Expert Analysis Tool
has plug in: FABBER
has plug in: BASIL
has plug in: VERBENA
has plug in: Brain Extraction Tool
has plug in: FMRIB's Automated Segmentation Tool
has plug in: FMRIB’s Integrated Registration and Segmentation Tool
has plug in: Harvard - Oxford Cortical Structural Atlas
has plug in: FMRIB's Linear Image Registration Tool
has plug in: FNIRT
has plug in: FSLVBM
has plug in: SIENA
has plug in: SIENAX
has plug in: Multimodal Image Segmentation Tool
has plug in: Brain Intensity AbNormality Classification Algorithm
has plug in: Multimodal Surface Matching
has plug in: fsl_anat
has plug in: FMRIB's Diffusion Toolbox
has plug in: Tract Based Spatial Statistics
has plug in: XTRACT
has plug in: eddy
has plug in: topup
has plug in: eddyqc
has plug in: randomise
has plug in: PALM
has plug in: fsl-cluster
has plug in: FDR
has plug in: DualRegression
has plug in: FLOBS
has plug in: FSLeyes
has plug in: Fslutils
has plug in: Atlasquery
has plug in: MCFLIRT
has plug in: POSSUM
has plug in: FSL-MRS
EPSRC ;
MRC ;
BBSRC ;
GlaxoSmithKline ;
Pfizer
PMID:21979382
PMID:19059349
PMID:15501092
Free, Available for download, Freely available nif-0000-00305, birnlex_2067, SCR_007368 http://www.nitrc.org/projects/fsl, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, https://sources.debian.org/src/fsl/ SCR_002823 , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library 2026-07-28 09:40:32 4685
Rainbow
 
Resource Report
Resource Website
10+ mentions
Rainbow (RRID:SCR_002724) software application, data analysis software, sequence analysis software, software resource, data processing software Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:22942077
DOI:10.1093/bioinformatics/bts482
Free, Freely available, Available for download SCR_015992, OMICS_03722, biotools:rainbow https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ SCR_002724 RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq 2026-07-28 09:40:30 41
nematodes.org
 
Resource Report
Resource Website
10+ mentions
nematodes.org (RRID:SCR_003267) nematodes.org data or information resource, organism-related portal, topical portal, portal Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes nematode, genomics, genome, gene, database, transcriptome, analysis tool, bioinformatics, genomics databases, software, expressed sequence tag, analysis, dna barcode, phylogenomics, FASEB list has parent organization: University of Edinburgh; Scotland; United Kingdom
is parent organization of: 959 Nematode Genomes
is parent organization of: MolluscDB PartiGene database
is parent organization of: NEMBASE
is parent organization of: PartiGene ARTHROPODA Database
is parent organization of: Bombus terrestris PartiGene Database
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03187 SCR_003267 Nematode & Neglected Genomics (at) The Blaxter Lab, Blaxter Lab, Nematode and Neglected Genomics, nematodes.org Nematode & Neglected Genomics (at) The Blaxter Lab, Nematode & Neglected Genomics 2026-07-28 09:40:39 30
GenePattern
 
Resource Report
Resource Website
1000+ mentions
GenePattern (RRID:SCR_003201) GenePattern software application, software resource, data analysis software, data processing software A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is affiliated with: GenePattern Notebook
is related to: TIGRESS
has parent organization: Broad Institute
NCI ;
NIGMS
PMID:16642009 Free, Freely available biotools:genepattern, OMICS_01855, nif-0000-30654 https://bio.tools/genepattern SCR_003201 2026-07-28 09:40:44 1078

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