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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Florida Alzheimer's Disease Research Center Resource Report Resource Website |
Florida Alzheimer's Disease Research Center (RRID:SCR_004940) | FADRC | data or information resource, disease-related portal, portal, topical portal | A statewide consortium dedicated to Alzheimer's disease research to better understand the disease and related memory disorders. It includes Alzheimer's researchers and clinicians from institutions across Florida such as USF Health, Mayo Clinic Jacksonville, and Mount Sinai Medical Center. The purpose of the ADRC is to assist institutions in developing an infrastructure (cores) that can be used for various research projects with the goal of better understanding Alzheimer's disease and related disorders. The Florida ADRC is comprised of six cores, three projects and three pilot projects among other collaborations that utilize these cores. | disease related portal, alzheimer's disease, memory disorder, dementia, clinical, late adult human |
is related to: Alzheimers Disease Genetics Consortium has parent organization: University of South Florida; Florida; USA is parent organization of: Mayo Clinic Jacksonville: Neuropathology and Microscopy |
Alzheimer's disease, Memory disorder, Dementia, Mild cognitive impairment | NIA RFA-AG-04-011 | Contact the core ADRC Administrator to use Florida ADRC cores | nlx_143954 | SCR_004940 | Florida ADRC, Florida Alzheimer's Disease Research Center | 2026-09-12 12:56:18 | 0 | |||||
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MBCluster.Seq Resource Report Resource Website 1+ mentions |
MBCluster.Seq (RRID:SCR_005079) | MBCluster.Seq | software resource | Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24191069 | GNU General Public License, >/=v3 | OMICS_01417, biotools:mbcluster.seq | https://bio.tools/mbcluster.seq | SCR_005079 | MBCluster.Seq: Model-Based Clustering for RNA-seq Data | 2026-09-12 12:56:20 | 1 | |||||
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University of Kansas; Kansas; USA Resource Report Resource Website 1+ mentions |
University of Kansas; Kansas; USA (RRID:SCR_005075) | KU | university | Public research university with its main campus in Lawrence, Kansas, and several satellite campuses, research and educational centers, medical centers, and classes across the state of Kansas. |
is parent organization of: HistoWeb: Nervous System is parent organization of: Images from the Clendening Library is parent organization of: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is parent organization of: DB-PABP: a database of polyanion binding proteins is parent organization of: Autism Genetic Database is parent organization of: University of Kansas Labs and Facilities is parent organization of: University of Kansas Protein Production Group Core Facility is parent organization of: University of Kansas Nuclear Magnetic Resonance Laboratory Core Facility is parent organization of: University of Kansas Molecular Graphics and Modeling Laboratory Core Facility is parent organization of: University of Kansas Medical Center; Kansas; USA is parent organization of: University of Kansas Lawrence Protein Structure and X-ray Crystallography Laboratory Core Facility is parent organization of: University of Kansas Microscopy and Analytical Imaging Research Resource Core Facility is parent organization of: University of Kansas Mass Spectrometry and Analytical Proteomics Core Facility is parent organization of: I-TASSER is parent organization of: University of Kansas Nanofabrication Core Facility is parent organization of: University of Kansas Flow Cytometry Core Facility |
ISNI:0000 0001 2106 0692, Wikidata:Q52413, nlx_83015, Crossref funder ID:100007859, grid.266515.3 | https://ror.org/001tmjg57 | SCR_005075 | University of Kansas | 2026-09-12 12:56:20 | 1 | ||||||||
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AGORA Resource Report Resource Website 100+ mentions |
AGORA (RRID:SCR_005070) | AGORA | software resource | An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences. | genome assembly, genome, reconstruction | is listed by: OMICtools | PMID:22856673 | OMICS_00039 | SCR_005070 | Assembly Guided by Optical Restriction Alignment | 2026-09-12 12:56:20 | 105 | |||||||
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GRASS Resource Report Resource Website 50+ mentions |
GRASS (RRID:SCR_005071) | GRASS | software resource | A generic algorithm for scaffolding next-generation sequencing assemblies. | next-generation sequencing, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22492642 | GNU General Public License, v3 | biotools:GRASS, OMICS_00043 | https://bio.tools/GRASS | SCR_005071 | GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies, GeneRic ASembly Scaffolder | 2026-09-12 12:56:20 | 89 | |||||
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Protocol Online - Your labs reference book Resource Report Resource Website 10+ mentions |
Protocol Online - Your labs reference book (RRID:SCR_004937) | Protocol Online | data or information resource, experimental protocol, narrative resource | Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert). | bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, database |
is used by: NIF Data Federation is used by: Integrated Blogs |
Eppendorf ; Invitrogen ; Chang Bioscience ; Mirus ; KPL ; Oligomaster ; Abcam ; Nature Publishing Group |
nlx_90492 | SCR_004937 | Protocol Online Your lab''s reference book, Protocol-Online | 2026-09-12 12:56:18 | 11 | |||||||
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MapAl Resource Report Resource Website 1+ mentions |
MapAl (RRID:SCR_004938) | MapAl | software resource | A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably. | rna?seq |
is listed by: OMICtools has parent organization: BOKU University; Vienna; Austria |
PMID:22485116 | GNU General Public License | OMICS_01261 | SCR_004938 | 2026-09-12 12:56:18 | 1 | |||||||
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SINA Resource Report Resource Website 100+ mentions |
SINA (RRID:SCR_005067) | SINA | analysis service resource, data analysis service, production service resource, service resource, software resource | Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation. | alignment, taxonomic classification, rrna, gene sequence, fasta, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SILVA is related to: ARB project has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:22556368 | Free, Available for download, Freely available | OMICS_01438, biotools:sina | https://bio.tools/sina, https://sources.debian.org/src/sina/, https://github.com/epruesse/SINA | SCR_005067 | SINA Alignment Service, SILVA Incremental Aligner | 2026-09-12 12:56:20 | 387 | |||||
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Bambus Resource Report Resource Website |
Bambus (RRID:SCR_005068) | Bambus | software resource | Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny. | scaffolding |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21926123 | Open unspecified license | OMICS_01432 | http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus | SCR_005068 | Bambus 2, Bambus 2.0 | 2026-09-12 12:56:20 | 0 | |||||
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Neuron Navigator Resource Report Resource Website |
Neuron Navigator (RRID:SCR_005063) | NNG | analysis service resource, d spatial image, data analysis service, data or information resource, database, production service resource, service resource | Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required. | image database, connectivity, drosophila, brain, neuron | has parent organization: National Tsing Hua University; Hsinchu; Taiwan | nlx_144057 | SCR_005063 | NNG: Neuron Navigator, NNG: Neuron Navigator - A Database of Drosophila Brain Neurons | 2026-09-12 12:56:20 | 0 | ||||||||
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University of Iowa Carver College of Medicine; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) | UI Carver College of Medicine | university | Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa. |
has parent organization: University of Iowa; Iowa; USA is parent organization of: MADS+ - discovery of differential splicing events from Affymetrix exon junction array data is parent organization of: University of Iowa College of Medicine Department of Pharmacology is parent organization of: University of Iowa Magnetic Resonance Research Facility is parent organization of: University of Iowa Center for Gene Therapy Vectore Core is parent organization of: University of Iowa Center for Gene Therapy Clinical Core is parent organization of: University of Iowa Center for Gene Therapy Animal Model Core is parent organization of: University of Iowa Center for Gene Therapy is parent organization of: University of Iowa Center for Gene Therapy Comparative Pathology Core is parent organization of: University of Iowa Center for Gene Therapy Cell Tissue Core |
nlx_68753 | SCR_005064 | University of Iowa Carver College of Medicine, Roy J. and Lucille A. Carver College of Medicine | 2026-09-12 12:56:20 | 1 | |||||||||
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/, https://bio.tools/g-blastn | SCR_005062 | 2026-09-12 12:56:20 | 0 | |||||
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SLIDE Resource Report Resource Website 10+ mentions |
SLIDE (RRID:SCR_005137) | SLIDE | software resource | Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NIH ; NHGRI HG004695; NHGRI HG005639; NEI EY019094 |
PMID:22135461 | OMICS_01291 | SCR_005137 | sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation | 2026-09-12 12:56:21 | 33 | |||||||
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VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-09-12 12:56:21 | 1 | |||||
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RetroSeq Resource Report Resource Website 10+ mentions |
RetroSeq (RRID:SCR_005133) | RetroSeq | software resource | A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences. | mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:23233656 | Acknowledgement requested, Open unspecified license | OMICS_11232, OMICS_00120 | SCR_005133 | 2026-09-12 12:56:21 | 46 | |||||||
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Cloudbreak Resource Report Resource Website |
Cloudbreak (RRID:SCR_005097) | software resource | Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features. | illumina, mapreduce, insertion, deletion, genomic | is listed by: OMICtools | OMICS_04078 | SCR_005097 | 2026-09-12 12:56:21 | 0 | ||||||||||
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Werblin Lab Resource Report Resource Website |
Werblin Lab (RRID:SCR_005251) | Werblin Lab | data or information resource, image, laboratory portal, organization portal, portal, video resource | The goal of our research is to uncover the neural circuitry that mediates some of the remarkable processing capabilities of the retina. The retina to operates at high spatial and temporal resolution over more than 7 orders of magnitude, to detect the direction of motion, to blank and then recover after saccades, to generate at least a dozen different abstract representations of the visual world. How is all of this, and much more, possible in this tissuepaper-thin array of neurons? Videos and images describing this include: * The retinal hypercircuit. * How the Retina Works * Take a Tour through the Retina * Cartoon of the retina showing layering of neurons * Directional Selectivity * Feedback and Crossover inhibition * Multiple Representations of the Visual Scene ** Pseudo Array Recording Methods ** Multiple Representations of the Visual World ** Regions of Frequency Space * Regions of space/time frequency * Space-time rasters for ON and OFF cells * Patching a neuron in a retinal slice * Targeting Retinal Neuron Subregions with Arficial Rhodopsins | retina, hypercircuit, neuron, ganglion | has parent organization: University of California at Berkeley; Berkeley; USA | nlx_144274 | SCR_005251 | Werblin Lab: Division of Neurobiology; Department of Molecular and Cell Biology | 2026-09-12 12:56:23 | 0 | ||||||||
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St. Louis University Alzheimer's Brain Bank Resource Report Resource Website |
St. Louis University Alzheimer's Brain Bank (RRID:SCR_005132) | biomaterial supply resource, brain bank, material resource, tissue bank | A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death. | brain bank, alzheimer's disease, normal control, dementia, brain tissue, autopsy, healthy donor, material storage repository |
is listed by: One Mind Biospecimen Bank Listing has parent organization: St. Louis University Department of Neurology and Psychiatry has parent organization: Saint Louis University School of Medicine; Missouri; USA |
Alzheimer's disease, Dementia | alz.org | Public, Available to the research community | nlx_144152 | SCR_005132 | SLU Brain Bank, Saint Louis University Alzheimer’s Brain Bank, Saint Louis University Medical Center Alzheimer's Disease Brain Bank | 2026-09-12 12:56:21 | 0 | ||||||
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Gene Map Annotator and Pathway Profiler Resource Report Resource Website 100+ mentions |
Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) | data processing software, data visualization software, software application, software resource | GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options. | expression, gene, analysis, biological, mapping, microarray, network, pathway, protein, visualization, ontology, proteomics, FASEB list |
has parent organization: University of California at San Francisco; California; USA is parent organization of: MAPPFinder |
Agilent Foundation ; BayGenomics ; NIGMS |
PMID:17588266 | nif-0000-00244 | SCR_005094 | GenMAPP | 2026-09-12 12:56:21 | 212 | |||||||
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Cereal Plant Development Ontology Resource Report Resource Website |
Cereal Plant Development Ontology (RRID:SCR_005095) | GRO-CPD | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157358 | http://www.gramene.org/plant_ontology/ | SCR_005095 | 2026-09-12 12:56:21 | 0 |
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