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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DRCAT Resource Catalogue Resource Report Resource Website 1+ mentions |
DRCAT Resource Catalogue (RRID:SCR_005931) | DRCAT | database, data or information resource, catalog | Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ''''Query'''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ''''Query'''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts. | metadata, bioinformatics, database, ontology, taxonomy, registry, annotation, data set |
is related to: EDAM Ontology has parent organization: European Bioinformatics Institute |
Acknowledgement required, See license | nlx_151280 | SCR_005931 | DRCAT (the data resource catalogue), DRCAT Resource Catalogue - Bioinformatics Web-based Data Resources, Data Resource Catalogue | 2026-08-08 11:58:39 | 2 | |||||||
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Genome Research Foundation Resource Report Resource Website 1+ mentions |
Genome Research Foundation (RRID:SCR_006056) | GRF, GF | institution | The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project | bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure |
has parent organization: Korean Ministry of Education Science and Technology is parent organization of: MetaBase |
Content is available under BioLicense: the freest license. | grid.410888.d, nlx_151458, Wikidata: Q5533483 | https://ror.org/03khjyh83 | SCR_006056 | Genome Foundation | 2026-08-08 11:58:33 | 1 | ||||||
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ScyTek Laboratories Resource Report Resource Website 100+ mentions |
ScyTek Laboratories (RRID:SCR_005919) | commercial organization | An Antibody supplier | nlx_152455 | SCR_005919 | 2026-08-08 11:58:50 | 109 | ||||||||||||
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Voronoia Resource Report Resource Website 10+ mentions |
Voronoia (RRID:SCR_006005) | database, data or information resource, software resource, software toolkit | Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins. | has parent organization: University Medicine Berlin; Berlin; Germany | nif-0000-03641 | http://141.42.202.21/voronoia/index.php | SCR_006005 | Voronoia | 2026-08-08 11:58:33 | 10 | |||||||||
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MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-08-08 11:58:39 | 40 | ||||||
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Quantum Dot Corporation Resource Report Resource Website |
Quantum Dot Corporation (RRID:SCR_005941) | commercial organization |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\ \\\\\\ An Antibody supplier |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152443 | SCR_005941 | 2026-08-08 11:58:39 | 0 | |||||||||||
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ProQuest Dissertation Publishing Resource Report Resource Website |
ProQuest Dissertation Publishing (RRID:SCR_006075) | ProQuest Dissertation Publishing | service resource | ProQuest Dissertation Publishing has been publishing dissertations and theses since 1938. In that time, we have published over 2 million graduate works from graduate schools around the world. We have over 700 active university publishing partners, and publish more than 70,000 new graduate works each year. In addition to publishing, we provide access to graduate works for thousands of libraries around the world. Based on your interests, you should find the information you need below: * Authors - Information for authors on why and how to publish their graduate work with us. * Grad Schools & Libraries - Learn about the benefits of publishing, and why to submit online. * Researchers - We can help you find the dissertation or thesis you need. | dissertation, publishing, thesis, graduate, library, research, author |
is related to: ProQuest Dissertations and Theses Global has parent organization: ProQuest |
nlx_151558 | SCR_006075 | 2026-08-08 11:58:33 | 0 | |||||||||
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Workflow4Ever Resource Report Resource Website 1+ mentions |
Workflow4Ever (RRID:SCR_005939) | Wf4Ever | knowledge environment | Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment. | preservation, workflow, provenance, archive, research object, workflow model, management, experimental method |
is listed by: FORCE11 is related to: myExperiment is related to: RightField |
European Union | nlx_151286 | SCR_005939 | 2026-08-08 11:58:32 | 1 | ||||||||
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University of North Texas; Texas; USA Resource Report Resource Website |
University of North Texas; Texas; USA (RRID:SCR_005935) | UNT | university | Public research university in Denton, Texas. | is related to: Alzheimers Disease Genetics Consortium | grid.266869.5, nlx_157964, Wikidata:Q860527, ISNI:0000 0001 1008 957X, Crossref funder ID:100008973 | https://ror.org/00v97ad02 | SCR_005935 | University of North Texas | 2026-08-08 11:58:32 | 0 | ||||||||
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ReproCELL Incorporated Resource Report Resource Website |
ReproCELL Incorporated (RRID:SCR_005973) | commercial organization | An Antibody supplier | nlx_152450 | SCR_005973 | 2026-08-08 11:58:32 | 0 | ||||||||||||
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BASH4RfMRI Resource Report Resource Website |
BASH4RfMRI (RRID:SCR_005970) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI. | algorithm or reusable library, information theory, spectral analysis, correlation, multivariate analysis, platform or development environment, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Analysis of Functional NeuroImages is related to: FreeSurfer is related to: 1000 Functional Connectomes Project |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151343 | SCR_005970 | BASH Scripts, bash-rs-fcmri | 2026-08-08 11:58:32 | 0 | ||||||||
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eQuilibrator Resource Report Resource Website 100+ mentions |
eQuilibrator (RRID:SCR_006011) | web application, database, data or information resource, software resource | Web interface designed for thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. It can provide estimates for compounds in the KEGG database, and individual compounds and enzymes can be searched for by their common names (water, glucosamine, hexokinase). Reactions can be entered in a free-text format that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations. | web interface, thermodynamics, biochemical system, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: KEGG |
Azrieli Foundation ; Israel Academy of Sciences and Humanities ; European Research Council 260392 - SYMPAC |
PMID:22064852 | Open source | nlx_151400, biotools:equilibrator | https://bio.tools/equilibrator | SCR_006011 | eQuilibrator - biochemical thermodynamics calculator | 2026-08-08 11:58:52 | 118 | |||||
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Doris Duke Charitable Foundation Resource Report Resource Website 10+ mentions |
Doris Duke Charitable Foundation (RRID:SCR_006012) | DDCF | institution | The mission of the Doris Duke Charitable Foundation is to improve the quality of people''s lives through grants supporting the performing arts, environmental conservation, medical research and the prevention of child abuse, and through preservation of the cultural and environmental legacy of Doris Duke''s properties. Established in 1996, the foundation supports four national grant-making programs. It also supports three properties that were owned by Doris Duke in Hillsborough, New Jersey; Honolulu, Hawaii; and Newport, Rhode Island. The foundation is headquartered in New York and is governed by a board of 12 Trustees. DDCF''s activities are guided by the will of Doris Duke, who endowed the foundation with financial assets that totaled approximately $1.6 billion as of December 31, 2010. The foundation regularly evaluates and modifies its allocation of resources from the endowment to support the programs and properties and to respond to fluctuations in portfolio returns. The foundation awarded its first grants in 1997. As of December 31, 2011, the foundation has awarded grants totaling more than $1 billion. DDCF awards grants in four core program areas: * The Arts Program supports performing artists with the creation and public performance of their work. * The Environment Program supports efforts that enable communities to protect and manage wildlife habitat and create efficient built environments. * The Medical Research Program seeks to contribute to the prevention and cure of disease by supporting clinical research. * The Child Abuse Prevention Program seeks to protect children from abuse and neglect in order to promote their healthy development. In the fall of 2007, DDCF also launched the African Health Initiative, with the goal of strengthening health systems in sub-Saharan Africa. The Building Bridges Program, which seeks to increase public understanding of Islamic cultures through media and the arts, is funded through the Doris Duke Foundation for Islamic Art and is headquartered in DDCF''s offices in New York. The Properties In her will, Doris Duke requested that several operating foundations manage the properties listed below. She also expressed her wishes that the properties be opened for public visitation and used for educational programs. The operating foundations receive funding from the Doris Duke Charitable Foundation. * The Duke Farms Foundation manages a 2,700-acre property in Hillsborough, New Jersey, which is known as Duke Farms and has a mission of environmental stewardship. * The Doris Duke Foundation for Islamic Art manages Doris Duke''s home in Honolulu, Hawaii, which is known as Shangri La and serves as a center for the study of Islamic art and cultures. * The Newport Restoration Foundation preserves historic houses in Newport, Rhode Island, and operates Doris Duke''s home in Newport known as Rough Point, which is also a public museum. | art, environment, medical research, child abuse, prevention, grant, african, health | nlx_151423, grid.453038.9, ISNI: 0000 0001 0570 6924, Crossref funder ID: 100000862 | https://ror.org/04n65rp89 | SCR_006012 | 2026-08-08 11:58:33 | 41 | |||||||||
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NOVA Biologics Resource Report Resource Website |
NOVA Biologics (RRID:SCR_005985) | commercial organization | An Antibody supplier | nlx_152422 | SCR_005985 | NOVA Biologics Inc., NOVA Biologics Inc | 2026-08-08 11:58:32 | 0 | |||||||||||
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GeneVito Resource Report Resource Website |
GeneVito (RRID:SCR_006211) | GeneVito | software resource, software application, data visualization software, data processing software | A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system. | java, genome-wide analysis, genome, visualization, gene, function, structure, dna, protein sequence, genomic, proteomic | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:14594459 | Free for academic use, Acknowledgement requested | nlx_151776 | SCR_006211 | GeneVito: Genome Visualization Tool, GeneViTo (Genome Visualization Tool), Genome Visualization Tool | 2026-08-08 11:58:56 | 0 | ||||||
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deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-08-08 11:58:56 | 34 | |||||
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Semantic MediaWiki Resource Report Resource Website 1+ mentions |
Semantic MediaWiki (RRID:SCR_006246) | SMW | software resource | A free, open-source extension to MediaWiki - the wiki software that powers Wikipedia - that helps to search, organize, tag, browse, evaluate, and share the wiki''s content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that allow a wiki to function as a collaborative database. Semantic MediaWiki introduces some additional markup into the wiki-text which allows users to add semantic annotations to the wiki. While this first appears to make things more complex, it can also greatly simplify the structure of the wiki, help users to find more information in less time, and improve the overall quality and consistency of the wiki. A large number of related extensions have been created that extend the ability to edit, display and browse through the data stored by SMW: the term Semantic MediaWiki is sometimes used to refer to this entire family of extensions. | extension, wiki, semantic annotation, authoring tool |
is listed by: FORCE11 has parent organization: MediaWiki |
European Union | Open unspecified license | nif-0000-06677 | SCR_006246 | Semantic Media Wiki | 2026-08-08 11:58:57 | 3 | ||||||
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pepStat Resource Report Resource Website 1+ mentions |
pepStat (RRID:SCR_006240) | software resource | Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. | standalone software | is listed by: OMICtools | PMID:23770318 | OMICS_04027 | SCR_006240 | 2026-08-08 11:58:56 | 8 | |||||||||
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PSCDB - Protein Structural Change DataBase Resource Report Resource Website |
PSCDB - Protein Structural Change DataBase (RRID:SCR_006116) | PSCDB | database, data or information resource, image collection | Database for protein structural change upon ligand binding that are classified into 7 classes in terms of the ligand binding sites and the location where the dominant motion occurs. # Coupled Domain motions are the domain motions induced upon ligand binding. # Independent Domain motions are the observable domain motions regardless of ligand binding. # Coupled Local motions are the local motions induced upon ligand binding. # Independent Local motions are the observable local motions regardless of ligand binding. # Burying ligand motions are imaginable motions required to hold ligand protein-inside. # No significant motions mean just nothing happen. # Other motions are motions unclassified into domain and local motions. Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. | protein, structure, ligand binding, ligand-free, ligand-bound, monomeric protein, homo-dimeric protein, animation, ligand, structural change | has parent organization: Nagoya University; Nagoya; Japan | Japanese Ministry of Education Culture Sports Science and Technology MEXT 20370063; Japanese Ministry of Education Culture Sports Science and Technology MEXT 21107523 |
PMID:22080505 PMID:21376729 |
nlx_151591 | SCR_006116 | Protein Structural Change DataBase (PSCDB), Protein Structural Change DataBase | 2026-08-08 11:58:54 | 0 | ||||||
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estMOI Resource Report Resource Website 10+ mentions |
estMOI (RRID:SCR_006192) | estMOI | software resource | A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt). | multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome | is listed by: OMICtools | PMID:24443379 | Free, Public | OMICS_02240 | SCR_006192 | estMOI - Estimating multiplicity of infection using parasite deep sequencing data | 2026-08-08 11:58:41 | 10 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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