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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneInfoViz Resource Report Resource Website |
GeneInfoViz (RRID:SCR_005680) | GeneInfoViz | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of gene relation networks. It takes a input list of genes in the form of LocusLink ID, UniGeneID, gene symbol, or accession number and returns their functional genomic information. Based on the GO annotations of the given genes, GeneInfoViz allows users to visualize these genes in the DAG structure of GO, and construct a gene relation network at a selected level of the DAG. Platform: Online tool | gene network, gene ontology, visualization, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:15724283 | Free for academic use | nlx_149121 | SCR_005680 | GeneInfoViz: Constructing and Visualizing Gene Relation Networks | 2026-02-12 09:44:08 | 0 | ||||||
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neuroVIISAS Resource Report Resource Website 1+ mentions |
neuroVIISAS (RRID:SCR_006010) | neuroVIISAS | software resource, d visualization software, software application, network graph visualization software, data processing software, data analytics software, data visualization software | An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS. | platform, simulation, mapping data, connectivity data, central nervous system, tracing, connectivity, java, image modality, pynest, nest, animation, brain, nervous system, brain mapping, neuroimaging, terminology, ontology, connectomics, atlas, population spike analysis, analytics, connectome, 3d visualization, visual analytics, ontology |
is listed by: 3DVC has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany |
PMID:22350719 | nlx_151398 | http://139.30.176.116/index-Dateien/Page455.htm | SCR_006010 | neuro Visualization Imagemapping Information System for Analysis and Simulation | 2026-02-12 09:44:22 | 8 | ||||||
|
modENCODE Resource Report Resource Website 100+ mentions |
modENCODE (RRID:SCR_006206) | modENCODE | analysis service resource, service resource, production service resource, data analysis service, data or information resource, data set | A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets. | epigenomics, epigenetics, genomics, functional element, model organism, genome, copy number variation, gene structure, genome sequence, histone modification, histone replacement, chromatin binding site, expression profiling, replication, transcription factor binding site, transcription factor, binding site, chromatin, rna, expression profiling, regulatory network, mrna, ncrna, dna replication, genotype |
is related to: ENCODE is related to: Encode |
NHGRI | PMID:19536255 | Public, With some restrictions on its use for 9 months following publication, Acknowledgement requested | nlx_151752 | SCR_006206 | NHGRI model organism ENCyclopedia Of DNA Elements, National Human Genome Research Institute model organism ENCyclopedia Of DNA Elements, model organism ENCyclopedia Of DNA Elements | 2026-02-12 09:44:19 | 255 | |||||
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UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource Resource Report Resource Website |
UAB Hepatorenal Fibrocystic Diseases Core Center Engineered Models Resource (RRID:SCR_015310) | service resource, access service resource, core facility, resource | Core whose goals include Generation of New Animal and Cell Models of HRFDs, to establish In Vivo Biosensors to Study Signaling Pathways Involved in HRFD Ciliopathies, and to generate and distribute HRFD Related Biologicals to the Center?s Investigator Base. | HRFD genes, engineered models |
is listed by: NIDDK Information Network (dkNET) has parent organization: UAB Hepatorenal Fibrocystic Diseases Core Center is organization facet of: UAB Hepatorenal Fibrocystic Diseases Core Center |
Hepatorenal Fibrocystic Disease | NIDDK P30DK074038 | Available to the research community, Acknowledgement requested | SCR_015310 | 2026-02-12 09:46:08 | 0 | ||||||||
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Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core Resource Report Resource Website |
Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester Model Systems Core (RRID:SCR_015312) | service resource, access service resource, core facility, resource | Core that makes available PKD model systems and technologies to PKD researchers at Mayo and at other institutions. Its services include C. elegans PKD-targeted services, Zebrafish PKD-targeted services, and Rodent PKD-targeted services. | model systems, c. elegans, zebrafish, rodents, PKD genes |
is listed by: NIDDK Information Network (dkNET) has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester is organization facet of: Translational Polycystic Kidney Disease (PKD) Center at Mayo Clinic Rochester |
Polycystic Kidney Disease | NIDDK P30DK090728 | Available to the research community | SCR_015312 | 2026-02-12 09:46:29 | 0 | ||||||||
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Sanford Burnham Prebys Medical Discovery Institute Model Organisms Resource Report Resource Website 1+ mentions |
Sanford Burnham Prebys Medical Discovery Institute Model Organisms (RRID:SCR_014853) | material resource, biomaterial supply resource | Facility that provides Drosophila melanogaster and Caenorhabditis elegans as model systems. It also provides training in how to manipulate the organisms and use equipment and provides technician assistance. | animal, drosophilia, fly, d melanogaster, c elegans, organisms | Commercially available | SCR_014853 | SBP Model Organisms, SBP Medical Discovery Institute Model Organisms | 2026-02-12 09:46:04 | 1 | ||||||||||
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GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | source code, software resource | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-02-12 09:43:25 | 576 | |||||
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Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | data or information resource, database, service resource | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2026-02-12 09:43:55 | 24 | ||||
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mirWIP Resource Report Resource Website 1+ mentions |
mirWIP (RRID:SCR_005055) | mirWIP | service resource, analysis service resource, production service resource, data analysis service | Tool to search for targets of conserved microRNAs in Caenorhabditis elegans by weighting RISC-immunoprecipitation-enriched parameters. | immunoprecipitation-enriched parameter, site, target, mirna, ribonucleoprotein, transcript |
is listed by: OMICtools has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:19160516 | OMICS_02284 | SCR_005055 | mirWIP - miRNA Targets by Weighting RISC-IP Enriched Parameters, miRNA targets by weighting immunoprecipitation-enriched parameters | 2026-02-12 09:44:02 | 4 | |||||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | service resource, analysis service resource, production service resource, data analysis service | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate https://bio.tools/funcassociate |
SCR_005768 | 2026-02-12 09:44:16 | 36 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | service resource, analysis service resource, production service resource, data analysis service | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-02-12 09:44:31 | 3 | ||||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | service resource, analysis service resource, production service resource, data analysis service | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-02-12 09:44:38 | 0 | |||
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HMMgene Resource Report Resource Website 10+ mentions |
HMMgene (RRID:SCR_011933) | HMMgene | service resource, analysis service resource, production service resource, data analysis service | Data analysis service for prediction of vertebrate and C. elegans genes. | gene |
is listed by: OMICtools has parent organization: CBS Prediction Servers |
OMICS_01488 | SCR_011933 | 2026-02-12 09:45:35 | 11 | |||||||||
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BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | service resource, analysis service resource, production service resource, data analysis service | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-02-12 09:45:46 | 45 |
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