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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DiscoTope Resource Report Resource Website 100+ mentions |
DiscoTope (RRID:SCR_018530) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web server to predict discontinuous B cell epitopes from protein three dimensional structures. | B cell epitope, B cell epitope prediction, discontinous B cell epitope prediction, protein, protein three dimentional structure, protein structure, 3D | European Union Seventh Framework Programme | PMID:23300419 | Free, Freely available | SCR_018530 | 2026-08-13 09:30:05 | 109 | |||||||||
|
AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin. | Allergen, allergen prediction, physicochemical protein property, protein, protein property, allergen exposure | National Research Fund of the Ministry of Education and Science ; Bulgaria |
PMID:23735058 | SCR_018496 | 2026-08-13 09:30:13 | 352 | ||||||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software toolkit, software resource | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-08-13 09:30:14 | 8 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software resource, software application | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-08-13 09:30:05 | 46 | ||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | data or information resource, application programming interface, data access protocol, web service, software resource | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-08-13 09:30:13 | 2 | |||||||
|
DIANA Tools Resource Report Resource Website 10+ mentions |
DIANA Tools (RRID:SCR_018425) | data or information resource, project portal, algorithm resource, database, service resource, software resource, portal | Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses. | miRNA data, miRNA regulatory element, miRNA target annotation, ncRNA, target prediction algorithm, miRNA target database, miRNA analysis |
has parent organization: University of Thessaly; Thessaly; Greece provides: DIANA microT-CDS provides: DIANA-mirExTra provides: DIANA-mirPath provides: TarBase provides: TarBase |
Free, Freely available | SCR_018425 | 2026-08-13 09:30:03 | 47 | ||||||||||
|
R scripts for FLIC data analysis Resource Report Resource Website 10+ mentions |
R scripts for FLIC data analysis (RRID:SCR_018386) | data analysis software, data processing software, software application, source code, software resource | R Code used to analyze FLIC data. Functions are provided to examine interactions with food for single well and food choice experiments when fly makes physical contact with liquid food. | Fly Liquid Food Interaction Counter, FLIC, FLIC data analysis, fly physical contact, liquid food fly interaction, data analysis | PMID:24978054 | Free, Available for download, Freely available | https://github.com/PletcherLab/FLIC_R_Code | SCR_018386 | R scripts for Fly Liquid Food Interaction Counter data analysis | 2026-08-13 09:30:22 | 14 | ||||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-08-13 09:30:05 | 109 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, software resource, service resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-08-13 09:30:14 | 34 | ||||||
|
Barzooka Resource Report Resource Website 1+ mentions |
Barzooka (RRID:SCR_018508) | algorithm resource, analysis service resource, production service resource, service resource, software resource | Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints. | Bar graph detection, continuous data, preprint, bioRxiv, bar graph, ASWG | PMID:35822444 | Free, Available for download, Freely available | SCR_018508 | 2026-08-13 09:30:13 | 5 | ||||||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data analysis software, data processing software, software application, data visualization software, software resource | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | 2026-08-13 09:30:04 | 11 | ||||||||||
|
CuGenDB Resource Report Resource Website 100+ mentions |
CuGenDB (RRID:SCR_018401) | CuGenDB | topical portal, data or information resource, database, portal | Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops. | Genomic data, genetic data, cucurbit, data distribution, data analysis, data mining, data integration, dataset, comparative genomics, functional genomics, cucurbit crop, FASEB list | USDA National Institute of Food and Agriculture Specialty Crop Research Initiative ; US-Israel Binational Agricultural Research and Development Fund ; USDA Agricultural Research Service ; International Cucurbit Genomics Initiative |
PMID:30321383 | Free, Freely available | SCR_018401 | Cucurbit Genomics Database, Cucurbitaceae family Genomics Database | 2026-08-13 09:30:12 | 285 | |||||||
|
Planmeca Romexis Resource Report Resource Website 1+ mentions |
Planmeca Romexis (RRID:SCR_018403) | data processing software, software application, image acquisition software, data acquisition software, software resource | Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility. | 3D imaging software, dental software, 3D image, dental | Restricted | SCR_018403 | 2026-08-13 09:30:23 | 1 | |||||||||||
|
Biorender Resource Report Resource Website 10000+ mentions |
Biorender (RRID:SCR_018361) | web application, service resource, software resource | Web tool for graphical illustrations for biological systems by BioRender. Used for articles and presentations. Collection of pre made icons and templates from life science fields for scientific illustrations. Customized icons possible on request. | Graphical illustration, biological system, pre made icon, pre made template, scientific illustration, customized icon | Restricted | SCR_018361 | 2026-08-13 09:30:22 | 26474 | |||||||||||
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Positional Gene Enrichment Resource Report Resource Website 1+ mentions |
Positional Gene Enrichment (RRID:SCR_018360) | PGE | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool implementing positional gene enrichment analysis of gene sets for high resolution identification of over represented chromosomal regions. | Fund for Scientific Research Flanders ; UGent |
PMID:18346969 | Free, Freely available | http://homes.esat.kuleuven.be/~bioiuser/pge/ | SCR_018360 | Positional Gene Enrichment, PGE analysis | 2026-08-13 09:30:02 | 1 | |||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | data analysis software, data processing software, software resource, software application | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-08-13 09:30:12 | 32 | ||||||||
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TinderMIX Resource Report Resource Website 1+ mentions |
TinderMIX (RRID:SCR_018364) | data analysis software, data processing software, software resource, software application | Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features. | Dose dependent gene expression, time dependent gene expression, gene expression analysis, dose response, cluster gene expression, contour plot, toxicogenomics data analysis, time point, dose level, expression pattern identification, data | Free, Available for download, Freely available | https://rdrr.io/github/angy89/TinderMIX/, https://github.com/angy89/TinderMIX/ | SCR_018364 | Time-Dose INtegrated moDelling of toxicogenomics data | 2026-08-13 09:30:22 | 1 | |||||||||
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PredGPI Resource Report Resource Website 10+ mentions |
PredGPI (RRID:SCR_018363) | data or information resource, data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes. | GPI anchored protein predictor, GPI anchored protein, predict presence of GPI anchor, predict position of omega site, discrimination of anchoring signal, prediction of probable omega site, data, screening whole proteome | European Union VI Framework Programme ; FIRB 2003 LIBI–International Laboratory of Bioinformatics |
PMID:18811934 | Free, Freely available | SCR_018363 | 2026-08-13 09:30:02 | 22 | |||||||||
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STARANISO Resource Report Resource Website 50+ mentions |
STARANISO (RRID:SCR_018362) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data. | Anisotropy, diffraction limit, Bayesian estimation, structure amplitude, Global Phasing Limited, anisotropic cut off, data, anisotropic correction data | Global Phasing Consortium | Free, Freely available | SCR_018362 | The STARANISO Server, STARANISO Server, STARANISO server | 2026-08-13 09:30:12 | 78 | |||||||||
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Conserved Domains Search Resource Report Resource Website 1000+ mentions |
Conserved Domains Search (RRID:SCR_018729) | data or information resource, data access protocol, service resource, web service, software resource | Web tool for conserved domains searching within protein or coding nucleotide sequence. | Conserved domain, protein, coding nucleotide sequence, domain search, domain, nucleotide sequence | works with: Conserved Domain Database | Free, Freely available | SCR_018729 | CD-search | 2026-08-13 09:30:28 | 2002 |
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