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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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University of Manchester; Manchester; United Kingdom Resource Report Resource Website 10+ mentions |
University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) | university | Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment. |
is affiliated with: OpenMinTeD is related to: NEWMEDS is related to: ORBITO is related to: Open PHACTS is related to: EMIF is parent organization of: Smart Dictionary Lookup is parent organization of: mlgt is parent organization of: Utopia Docs is parent organization of: Kidney and Urinary Pathway Knowledge Base is parent organization of: PUMA is parent organization of: DOSY Toolbox is parent organization of: RightField is parent organization of: SEEK is parent organization of: miRBase is parent organization of: PRINTS is parent organization of: CHEM21 is parent organization of: Taverna is parent organization of: SysMO-DB is parent organization of: MethodBox is parent organization of: OWL API is parent organization of: X:MAP is parent organization of: Mimas is parent organization of: National Centre for Text Mining is parent organization of: Chemistry Using Text Annotations is parent organization of: TerMine is parent organization of: Acromine Disambiguator is parent organization of: Census Dissemination Unit is parent organization of: Open Regulatory Annotation Database is parent organization of: ADAPT: A Database of Affymetrix Probesets and Transcripts is parent organization of: brat rapid annotation tool is parent organization of: UK DNA Banking Network is parent organization of: AcroMine is parent organization of: BioIE: Extracting Informative Sentences From the Biomedical Literature is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: myExperiment is parent organization of: Software Ontology is parent organization of: bioNerDS is parent organization of: MorphoJ is parent organization of: University of Manchester Bioinformatics Core Facility is parent organization of: miRBase is parent organization of: Simple Assignment of Spots to Surfaces is parent organization of: AMBER parameter database is parent organization of: University of Manchester Electron Microscopy Core Facility is parent organization of: University of Manchester Mass Spectrometry and Separations Core Facility is parent organization of: University of Manchester Advanced Manufacturing Platform Core Facility is parent organization of: University of Manchester Surface Characterisation Core Facility is parent organization of: University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility is parent organization of: University of Manchester Corrosion and Materials for Demanding Environments Core Facility is parent organization of: University of Manchester Magnetic Resonance and Related Technology Platform Core Facility is parent organization of: University of Manchester X-ray Diffraction Platform Core Facility is parent organization of: University of Manchester Services and Equipment Core Facility is parent organization of: University of Manchester Design, Fabrication and Testing Core Facility is parent organization of: University of Manchester National X-ray Computed Tomography Core Facility is parent organization of: University of Manchester Advanced Metal Development Core Facility is parent organization of: University of Manchester BioAutomation and Biofoundry Core Facility is parent organization of: University of Manchester Biomolecular NMR Core Facility has organization facet: MANC-RISK-SCREEN |
nlx_74265, Wikidata:Q230899, grid.5379.8, ISNI:121662407, Crossref funder ID:501100000770 | https://ror.org/027m9bs27 | SCR_004996 | University of Manchester | 2026-09-12 12:56:19 | 10 | |||||||||
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Bio X Cell Resource Report Resource Website 1000+ mentions |
Bio X Cell (RRID:SCR_004997) | commercial organization | Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services. | commercial, antibody, reagent, biomedical, research, new hampshire, | SCR_019248, nlx_152318 | SCR_004997 | 2026-09-12 12:56:19 | 4386 | |||||||||||
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ESPRIT-Tree Resource Report Resource Website 1+ mentions |
ESPRIT-Tree (RRID:SCR_005045) | ESPRIT-Tree | software resource | Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time. | clustering, 16s rrna, pyrosequence |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:21596775 | OMICS_01445 | SCR_005045 | ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time | 2026-09-12 12:56:20 | 9 | |||||||
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Huazhong University of Science and Technology; Wuhan; China Resource Report Resource Website 1+ mentions |
Huazhong University of Science and Technology; Wuhan; China (RRID:SCR_005047) | HUST | university | Public research university located in Guanshan Subdistrict, Hongshan District, Wuhan, Hubei province, China. |
is parent organization of: AnimalTFDB is parent organization of: Midbody, Centrosome and Kinetochore is parent organization of: EPSD Eukaryotic Phosphorylation Site Database |
ISNI:0000 0004 0368 7223, grid.33199.31, Wikidata:Q1711196, nlx_144495, Crossref funder ID:501100003397 | https://ror.org/00p991c53 | SCR_005047 | Huazhong University of Science and Technology, Huazhong University of Science & Technology, Huazhong University of Science & Technology; Hubei; China | 2026-09-12 12:56:20 | 5 | ||||||||
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Ivy Glioblastoma Atlas Project Resource Report Resource Website 100+ mentions |
Ivy Glioblastoma Atlas Project (RRID:SCR_005044) | Ivy GAP | atlas, data or information resource, database, image collection | Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment. | glioblastoma, in situ hybridization, hematoxylin and eosin stain, brain, tumor, gene expression, anatomic structure, histology, clinical, genomic, expression array, gene, FASEB list | has parent organization: Allen Institute for Brain Science | Brain cancer, Cancer | Ben and Catherine Ivy Foundation | nlx_99161 | SCR_005044 | 2026-09-12 12:56:20 | 158 | |||||||
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Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets Resource Report Resource Website 1000+ mentions |
Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets (RRID:SCR_005040) | data or information resource, database, software resource | Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available. | worm, yeast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:17952086 | biotools:percolator, nlx_98814 | https://bio.tools/percolator | SCR_005040 | Percolator | 2026-09-12 12:56:20 | 2729 | |||||||
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Brain Research Institute Resource Report Resource Website |
Brain Research Institute (RRID:SCR_004988) | BRI | data or information resource, graduate program resource, portal, postdoctoral program resource, topical portal, training resource | Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches. | one mind tbi, one mind ptsd, neuroscience, nervous system, genomics, proteomics, magnetic resonance imaging assay, positron emission tomography, biosensor, microelectromechanical system, brain, spinal cord |
has parent organization: University of California at Los Angeles; California; USA is parent organization of: Numerical Fibre Generator is parent organization of: cortex is parent organization of: SOCK is parent organization of: Brain Research Institute Biobank Resources |
Brain disorder, Parkinson's disease, Huntington's disease, Alzheimer's disease, Neurofibromatosis, Stroke, Spinal cord injury, Traumatic brain injury, Post-Traumatic Stress Disorder | nlx_143995 | http://www.bri.ucla.edu/index_02.asp | SCR_004988 | Brain Research Institute UCLA | 2026-09-12 12:56:19 | 0 | ||||||
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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 | |||||||||
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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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