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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BIOBASE Corporation Resource Report Resource Website 100+ mentions |
BIOBASE Corporation (RRID:SCR_010271) | commercial organization | THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database. | FASEB list |
is related to: Human Gene Mutation Database is parent organization of: Genome Trax is parent organization of: TRANSPATH is parent organization of: Gene Regulation Programs is parent organization of: TRANSCompel is parent organization of: Gene Regulation Databases |
THIS RESOURCE IS OUT OF SERVICE | nlx_156933 | SCR_010271 | 2026-02-14 02:01:55 | 183 | |||||||||
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Bionutrition Ontology Resource Report Resource Website 1+ mentions |
Bionutrition Ontology (RRID:SCR_010272) | BNO | data or information resource, ontology, controlled vocabulary | Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting. | owl | is listed by: BioPortal | nlx_157337 | SCR_010272 | 2026-02-14 02:01:55 | 1 | |||||||||
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HHpred Resource Report Resource Website 500+ mentions |
HHpred (RRID:SCR_010276) | data or information resource, software resource, database | The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred. | nlx_156935 | SCR_010276 | Homology detection & structure prediction by HMM-HMM comparison | 2026-02-14 02:01:56 | 972 | |||||||||||
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BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq https://sources.debian.org/src/bitseq/ |
SCR_009904 | 2026-02-14 02:01:42 | 19 | |||||||
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U.S. Department of Labor Resource Report Resource Website 1+ mentions |
U.S. Department of Labor (RRID:SCR_010157) | DOL | institution | Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights. | grid.420412.1, nlx_151864, ISNI: 0000 0001 2097 824X, Wikidata: Q628807, Crossref funder ID: 100000778 | https://ror.org/05mbkbj54 | SCR_010157 | US Dept. of Labor, US DOL, US Department of Labor, United States Department of Labor | 2026-02-14 02:01:55 | 1 | |||||||||
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BioTop Ontology Resource Report Resource Website 1+ mentions |
BioTop Ontology (RRID:SCR_010039) | BT | data or information resource, ontology, controlled vocabulary | A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. It can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones. | owl | is listed by: BioPortal | nlx_157329 | http://purl.org/biotop | SCR_010039 | 2026-02-14 02:01:43 | 1 | ||||||||
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Enzyme Mechanism Ontology Resource Report Resource Website 1+ mentions |
Enzyme Mechanism Ontology (RRID:SCR_010315) | EMO | data or information resource, ontology, controlled vocabulary | Ontology to describe the active components of the enzyme''s reactions (cofactors, amino acid residues and cognate ligands) and their roles in the reaction. EMO builds upon this by formalizing key concepts, and the relationships between them, necessary to define enzymes and their functions. This describes not only the general features of an enzyme, including the EC number (catalytic activity), 3D structure and cellular locations, but also allows for the detailed annotation of the mechanism. This mechanistic detail can be either at a gross level (overall reaction only), or the more detailed granularity of the steps and components required to effect the overall chemical transformation. | owl | is listed by: BioPortal | nlx_157397 | SCR_010315 | 2026-02-14 02:01:57 | 1 | |||||||||
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Enzyme Reaction Ontology for partial chemical perspectives Resource Report Resource Website 1+ mentions |
Enzyme Reaction Ontology for partial chemical perspectives (RRID:SCR_010316) | PIERO | data or information resource, ontology, controlled vocabulary | An enzyme ontology that deals with partial reactions (transformations) | owl | is listed by: BioPortal | nlx_157398 | SCR_010316 | 2026-02-14 02:01:44 | 1 | |||||||||
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Johns Hopkins University; Maryland; USA Resource Report Resource Website 10+ mentions |
Johns Hopkins University; Maryland; USA (RRID:SCR_010247) | JHU | university | Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins. | private, university, Baltimore, Maryland |
uses: DIRECT2experts is affiliated with: Diabetes Research Centers is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: ABX Guide is related to: Clinical and Translational Science Awards Consortium is parent organization of: SynaptomeDB is parent organization of: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA is parent organization of: sim4cc is parent organization of: MRI Studio is parent organization of: CKID A Prospective Cohort Study of Kidney Disease in Children is parent organization of: Nonalcoholic Steatohepatitis Clinical Research Network is parent organization of: ASprofile is parent organization of: GlimmerHMM is parent organization of: Neurogenetics and Behavior Center is parent organization of: Human Proteinpedia is parent organization of: Schramm Lab Spinal Cord Atlases is parent organization of: NetPath is parent organization of: Academic Drug Discovery Consortium is parent organization of: CardioVascular Research Grid (CVRG) is parent organization of: Johns Hopkins University; Undergraduate Neuroscience Program is parent organization of: Bowtie is parent organization of: FLASH is parent organization of: TMAJ is parent organization of: Gastroparesis Clinical Research Consortium is parent organization of: HPRD - Human Protein Reference Database is parent organization of: Atlweb: Alternatives to Animal Testing is parent organization of: Center for Inherited Disease Research is parent organization of: The Protein Coil Library is parent organization of: HIV Guide is parent organization of: Johns Hopkins School of Medicine Department of Molecular and Comparative Pathobiology is parent organization of: Classic Articles in Visual Perception is parent organization of: Experimental Man Blog is parent organization of: MYC Cancer Gene is parent organization of: JIST: Java Image Science Toolkit is parent organization of: DOTS WM tract segmentation is parent organization of: JHU Proj. in Applied Medical Imaging is parent organization of: LDDMM is parent organization of: Johns Hopkins Bloomberg School of Public Health; Maryland; USA is parent organization of: Genetic Resources Core Facility is parent organization of: LS-SNP/PDB is parent organization of: JHU Deep Sequencing and Microarray Core is parent organization of: Glimmer is parent organization of: Johns Hopkins University Labs and Facilities is parent organization of: CRAVAT is parent organization of: John Hopkins University, In-Vivo Cellular Molecular Imaging Center is parent organization of: RosettaDock is parent organization of: CoGAPS is parent organization of: Blox is parent organization of: National Resource for Quantitative Functional MRI is parent organization of: Myrna is parent organization of: CAWorks is parent organization of: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data is parent organization of: Longitudinal MS Lesion Imaging Archive is parent organization of: Image Synthesis Tools is parent organization of: Atlases of amygdala and hippocampus for pediatric populations is parent organization of: HISAT2 is parent organization of: neurodata is parent organization of: Johns Hopkins University Integrated Imaging Center Core Facility is parent organization of: Center for Computational Biology at JHU is parent organization of: TopHat is parent organization of: PyRosetta is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Johns Hopkins University School of Medicine Genetic Resources Core Facility |
nlx_97251, , Wikidata: Q193727, GRID: grid.21107.35, ISNI: 0000 0001 2171 931, Crossref Funder ID: 100007880 | https://ror.org/00za53h95 | SCR_010247 | 2026-02-14 02:01:54 | 12 | ||||||||
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UCL Bioinformatics Group Resource Report Resource Website 100+ mentions |
UCL Bioinformatics Group (RRID:SCR_010248) | software repository, portal, data or information resource, organization portal, software resource | Group headed by Professor David Jones, and was originally founded as the Joint Research Council funded Bioinformatics Unit within the Department of Computer Science at University College London. Supports the following tools: Protein Structure Prediction Threading (THREADER) Ab initio folding simulations Secondary structure prediction (PSIPRED) Protein disorder prediction (DISOPRED) Protein domain prediction (DomPred) Database of protein disorder (DisoDB) Protein Sequence Analysis Protein function prediction (ffpred) Metsite: Metal binding residue prediction HSPred : Protein-protein interaction characterisation Amino acid substitution matrices Hidden Markov Models (collaboration with N. Goldman, Cambridge, & J. Thorne, NCSU) Genome Analysis Genomic fold recognition (GenTHREADER) Genome annotation using software agents Protein Structure Classification CATH (collaboration with J. Thornton & C. Orengo, UCL Biochemistry) Transmembrane Protein Modelling MEMSAT & MEMSATSVM Folding In Lipid Membranes (FILM) MEMPACK Biological Applications of Data-mining and Machine Learning Techniques Information extraction for biological research (BioRat) Microarray Analysis Data integration for microarray analysis Data visualization Systems Biology Systems biology applied to stem cells Legacy Services (to be retired shortly) Comparison of structure classifications (CATH/SCOP/FSSP) Genomic Threading Database (GTD) | FASEB list | has parent organization: University College London; London; United Kingdom | nlx_156885 | SCR_010248 | 2026-02-14 02:01:55 | 190 | ||||||||||
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VassarStats Resource Report Resource Website 500+ mentions |
VassarStats (RRID:SCR_010263) | software resource | Tools for performing statistical computation including: Clinical Research Calculators Probabilities Distributions Frequency Data Proportions Ordinal Data Correlation & Regression t-Tests & Procedures ANOVA ANCOVA | has parent organization: Vassar College; New York; USA | nlx_156916 | SCR_010263 | VassarStats: Website for Statistical Computation | 2026-02-14 02:01:56 | 965 | ||||||||||
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TrueSight Resource Report Resource Website 1+ mentions |
TrueSight (RRID:SCR_009835) | TrueSight | software resource | Self-training Algorithm for Splice Junction Detection using RNA-seq. | is listed by: OMICtools | OMICS_01258 | SCR_009835 | 2026-02-14 02:01:53 | 2 | ||||||||||
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Leaf Senescence Database Resource Report Resource Website 1+ mentions |
Leaf Senescence Database (RRID:SCR_010227) | LSD | data repository, storage service resource, data or information resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019. Database of leaf senescence to collect SAGs, mutants, phenotypes and literature references. Leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes called SAGs. By integrating the data from mutant studies and transgenic analysis, they collected many SAGs related to regulation of the leaf senescence in various species. Additionally, they have categorized SAGs according to their functions in regulation of leaf senescence and used standard criteria to describe senescence associated phenotypes for mutants. Users are welcome to submit the new SAGs. | gene, mutant, leaf, phenotype, blast, plant development, sag | has parent organization: Peking University; Beijing; China | Senescence, Aging | Postdoctoral Fellowship at Peking-Tsinghua Center for Life Sciences ; Ministry of Science and Technology of China 2009CB119101; Ministry of Agriculture of China 2010ZX08010-002; Natural Science Foundation of China 31071160; China Postdoctoral Science Foundation 2012M520108; China Postdoctoral Science Foundation 2013T60031 |
PMID:24185698 PMID:21097471 |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156775 | SCR_010227 | 2026-02-14 02:01:54 | 7 | |||||
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BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | sequence analysis software, data processing software, software repository, data analysis software, software application, software resource | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library https://bio.tools/beast https://sources.debian.org/src/beast-mcmc/ |
http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-02-14 02:01:55 | 6460 | ||||||
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Biological Imaging Methods Ontology Resource Report Resource Website 1+ mentions |
Biological Imaging Methods Ontology (RRID:SCR_010235) | FBbi | data or information resource, ontology, controlled vocabulary | A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. | obo |
is listed by: BioPortal has parent organization: Cell Image Library (CIL) |
nlx_157334 | SCR_010235 | 2026-02-14 02:01:55 | 1 | |||||||||
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WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | data access protocol, software resource, web service, service resource | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; Searle Scholars program ; NIGMS P50 GM62412 |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/ https://bio.tools/weblogo_3 |
SCR_010236 | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-02-14 02:01:55 | 3653 | |||||
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Purl Resource Report Resource Website 100+ mentions |
Purl (RRID:SCR_010238) | data or information resource, narrative resource, standard specification | Web addresses that act as permanent identifiers in the face of a dynamic and changing Web infrastructure. Instead of resolving directly to Web resources, PURLs provide a level of indirection that allows the underlying Web addresses of resources to change over time without negatively affecting systems that depend on them. This capability provides continuity of references to network resources that may migrate from machine to machine for business, social or technical reasons. | nlx_156858 | SCR_010238 | Persistent Uniform Resource Locators | 2026-02-14 02:01:43 | 208 | |||||||||||
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Swiss Commission for Technology and Innovation Resource Report Resource Website 1+ mentions |
Swiss Commission for Technology and Innovation (RRID:SCR_010084) | CTI | government granting agency | SCR_010084 | Commission for Technology and Innovation CTI, Commission for Technology and Innovation, Swiss Commission for Technology Innovation, Swiss Commission for Technology and Innovation CTI | 2026-02-14 02:01:54 | 1 | ||||||||||||
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Computational Biology and Functional Genomics Laboratory at Harvard Resource Report Resource Website 100+ mentions |
Computational Biology and Functional Genomics Laboratory at Harvard (RRID:SCR_010240) | software resource | A computational biology laboratory that builds and redistributes genetic software tools. |
has parent organization: Harvard University; Cambridge; United States is parent organization of: GeneSigDB |
nlx_156871 | SCR_010240 | Quackenbush Lab | 2026-02-14 02:01:55 | 221 | ||||||||||
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ieeg.org Resource Report Resource Website 50+ mentions |
ieeg.org (RRID:SCR_010000) | data repository, storage service resource, data or information resource, service resource, database | Repository for EEG data. The International Epilepsy Electrophysiology Portal is a collaborative initiative funded by the National Institutes of Neurological Disease and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. The portal includes a large database of scientific data and tools to analyze these datasets. | data sharing, FASEB list | Epilepsy | NINDS 1 U24 NS063930-01 | nlx_157297 | SCR_010000 | International Epilepsy Electrophysiology Portal, IEEG | 2026-02-14 02:01:53 | 51 |
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