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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Mental Functioning Ontology Resource Report Resource Website 1+ mentions |
Mental Functioning Ontology (RRID:SCR_003245) | MF, MFO | ontology, data or information resource, controlled vocabulary | An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies. | mental functioning, mental process, cognition, trait, psychology, neuroscience, owl |
is listed by: BioPortal is listed by: Google Code is listed by: OBO is related to: Information Artifact Ontology is related to: Emotion Ontology is related to: Emotion Ontology has parent organization: University at Buffalo; New York; USA |
Free, Freely available | nlx_157305 | http://purl.obolibrary.org/obo/mf.owl | SCR_003245 | mental-functioning-ontology | 2026-08-15 11:22:29 | 1 | ||||||
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MetaLocGramN Resource Report Resource Website 1+ mentions |
MetaLocGramN (RRID:SCR_003154) | MetaLocGramN | production service resource, data analysis service, web service, data access protocol, software resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice. | subcellular localization, protein, prediction, sequence, analysis, gram-negative protein, gram-negative, gram-negative bacteria |
is listed by: OMICtools is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: International Institute of Molecular and Cell Biology; Warsaw; Poland |
PMID:22705560 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01626 | SCR_003154 | 2026-08-15 11:22:24 | 3 | |||||||
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GeneCruiser Resource Report Resource Website 1+ mentions |
GeneCruiser (RRID:SCR_003153) | GeneCruiser | data access protocol, software resource, service resource, web service | A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources. | gene, genetic variation, probe, variation, annotation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Broad Institute |
PMID:16030072 | Free, Freely available | OMICS_00760 | https://www.broadinstitute.org/publications/broad3691 | SCR_003153 | 2026-08-15 11:22:25 | 4 | ||||||
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HUPO Proteomics Standards Initiative Resource Report Resource Website 10+ mentions |
HUPO Proteomics Standards Initiative (RRID:SCR_003158) | HUPO PSI | standard specification, controlled vocabulary, ontology, data or information resource, meeting resource, training resource, knowledge environment, narrative resource | Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO). | proteomics, work group, gel electrophoresis, mass spectrometry, molecular interaction, protein modification, proteomics informatics, sample processing, controlled vocabulary, miape, transcriptome, metabolome, proteome, metadata, mass spectrometry informatics, community standards, annotation system, protein-protein interaction, protein, data format, annotation, minimal reporting requirement, nomenclature, reporting guideline, data exchange format, ontology development, rdf development, FASEB list |
is listed by: OMICtools is related to: Proteomics Identifications (PRIDE) has parent organization: HUPO - Human Proteome Organisation is parent organization of: Mass Spectrometry Ontology is parent organization of: mzML is parent organization of: PSICQUIC Registry is parent organization of: Protein-Protein Interaction Ontology is parent organization of: Sample Processing and Separation Techniques Ontology |
Free, Freely available | nif-0000-00568, OMICS_01781 | SCR_003158 | The HUPO Proteomics Standards Initiative | 2026-08-15 11:22:25 | 46 | |||||||
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Hyperphagia Resource Report Resource Website 1+ mentions |
Hyperphagia (RRID:SCR_003157) | Hyperphagia | funding resource | Request for Applications to fund the best ideas in the field of hyperphagia research. Institutions of Higher Education, Nonprofit organizations, For-profit companies are eligible. | hyperphagia | Prader-Willi Syndrome | One SMALL Step | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156857 | SCR_003157 | Best Idea Grants in Hyperphagia Research, Best Idea Grants (BIG) in Hyperphagia Research | 2026-08-15 11:22:27 | 1 | ||||||
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miRBase Resource Report Resource Website 10000+ mentions |
miRBase (RRID:SCR_003152) | miRBase | database, naming service, data repository, storage service resource, data or information resource, service resource | Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation. | gene, annotation, hairpin, microrna, nomenclature, rna, sequence, target, transcript, unique name, mirna registry, genetics, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: University of Manchester; Manchester; United Kingdom |
BBSRC ; Wellcome Trust Sanger Institute |
PMID:24275495 PMID:21037258 PMID:20205188 PMID:17991681 PMID:16957372 PMID:16381832 PMID:14681370 |
Free, Available for download, Freely available | SCR_017497, r3d100010670, nif-0000-03134, biotools:mirbase | http://microrna.sanger.ac.uk/, https://bio.tools/mirbase, https://doi.org/10.17616/R3VG8D | SCR_003152 | microRNA database | 2026-08-15 11:22:27 | 10387 | ||||
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Research Network in Early Experience and Brain Development Resource Report Resource Website 10+ mentions |
Research Network in Early Experience and Brain Development (RRID:SCR_003271) | Research Network on Early Experience and Brain Development | image collection, data or information resource, portal, topical portal | Portal on how the experiences of early childhood are incorporated into the structures of the developing brain, and how, in turn, those changes in the structures of the brain influence behavior. The network explores how knowledge of brain development can guide us in understanding of behavioral development and vice versa. It focuses specifically on sensitive periods and neural plasticity, the reciprocal phenomena whereby (a) the brain is negatively affected if certain experiences fail to occur within a certain time period, and (b) the brain is altered by experience at virtually any point in the life span. Here we consider not only how the structure of experience is incorporated into the structure of the brain, but also how this knowledge can influence the decisions we make about intervening in the lives of children. Research and other projects conducted by the Network fall into four broad categories: * Effects of early experience on brain development * New methods for studying brain-behavior relations * Comparative studies of early brain-behavioral development * Impact on public policy: Educating educators and the media RESOURCES NimStim Face Stimulus Set The Research Network on Early Experience and Brain Development has developed a battery of 646 facial expression stimuli for use in its own and other studies of face and emotion recognition. Images include the following expressions, displayed by a variety of models of various genders and races: fearful, happy, sad, angry, surprised, calm, neutral, disgusted. They are making these stimuli available to the public free of charge with registration and acceptance of the terms and conditions to use the stimulus set. | brain, development, developing brain, behavior, early experience, brain development, facial expression stimuli, emotion, stimuli, facial expression, young human, child |
has parent organization: University of California at Davis; California; USA has parent organization: University of Pittsburgh; Pennsylvania; USA has parent organization: Oregon Health and Science University; Oregon; USA has parent organization: University of California at San Francisco; California; USA has parent organization: University of Maryland; Maryland; USA has parent organization: Stanford University; Stanford; California has parent organization: Vanderbilt University; Tennessee; USA has parent organization: Brandeis University; Massachusetts; USA has parent organization: University of California at Los Angeles; California; USA has parent organization: Tulane University; Louisiana; USA has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
James S. McDonnell Foundation ; MacArthur Foundation |
Free, Freely available | nif-0000-31447 | http://www.macbrain.org/faces/indexhtm | SCR_003271 | Research Network in Early Experience Brain Development | 2026-08-15 11:22:30 | 49 | |||||
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Geospiza Resource Report Resource Website 100+ mentions |
Geospiza (RRID:SCR_003264) | Geospiza | commercial organization, production service resource, software resource, material service resource, service resource | Developer of enterprise-class software systems for workflow management of genetic analysis. Geospiza has established itself as the life science industry's top software developer for meeting the combined laboratory, data management and analytical needs of biotechnology and pharmaceutical companies, universities, researchers, contract core and diagnostic laboratories involved in genetic testing and manufacturing bio-therapeutics. Geospiza's products are designed and built by biologists, enabling researchers to focus on the science, not the software. *GeneSifter Analysis Edition: Access easy-to-use statistical, visualization and annotation tools for Microarray and Next Generation Sequencing data. *GeneSifter Lab Edition: Manage cross-platform core lab operations from a single interface out-of-the-box. | genetic analysis, microarray, next generation sequencing, data management |
is listed by: OMICtools is parent organization of: FinchTV |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01127, nif-0000-31431 | http://www.geospiza.com/finchtv.html | SCR_003264 | Geospiza Inc. | 2026-08-15 11:22:29 | 130 | ||||||
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ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | ORFprimer - primer design for ORFs | 2026-08-15 11:22:27 | 1 | |||||||
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NESbase Resource Report Resource Website 1+ mentions |
NESbase (RRID:SCR_003268) | NESbase | database, data repository, storage service resource, data or information resource, service resource | Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Error reports and submissions of new data are most welcome! | nuclear export signal, protein, leucine | has parent organization: DTU Center for Biological Sequence Analysis | Danish National Research Foundation ; John and Birthe Meyer Foundation |
PMID:12520031 | Free, Available for download, Freely available | nif-0000-03188 | https://services.healthtech.dtu.dk/datasets/NESbase-1.0/ | SCR_003268 | 2026-08-15 11:22:30 | 7 | |||||
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Gene Expression Profiling in Spinal Cord Injury Resource Report Resource Website 100+ mentions |
Gene Expression Profiling in Spinal Cord Injury (RRID:SCR_003260) | data or information resource, database, data set | Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip. | database, spinal cord, contusion, microarray data, FASEB list | has parent organization: Rutgers University; New Jersey; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00011 | SCR_003260 | 2026-08-15 11:22:27 | 394 | |||||||||
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ResearchMaps Resource Report Resource Website 1+ mentions |
ResearchMaps (RRID:SCR_003178) | ResearchMaps | web application, software resource | UCLA based service for research planning aimed to help users integrate and summarize large amounts of information into a searchable graphic format. The interactive features facilitates planning during writing of grants, research papers and reviews. ResearchMaps can also be used as a collaborative tool and as a catalyst for the creative process. | research planning, grant writing, research paper, review writing | has parent organization: University of California at Los Angeles; California; USA | PMID:29723213 | Free, Freely available | nlx_156891 | SCR_003178 | 2026-08-15 11:22:25 | 3 | |||||||
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Gemi Resource Report Resource Website 10+ mentions |
Gemi (RRID:SCR_003211) | Gemi | software resource | Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences. | polymerase chain reaction, primer, pcr primer design, pcr primer, dna sequence, rna sequence, c#, .net/mono, windows, probe, multiple aligned sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23316117 | Free, Available for download, Freely available | OMICS_02332 | SCR_003211 | Gemi - PCR oligos / primers design from multiple sequence alignments | 2026-08-15 11:22:25 | 13 | ||||||
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MAUDS Resource Report Resource Website 1+ mentions |
MAUDS (RRID:SCR_003175) | MAUDS | data processing software, software application, data analysis software, source code, software resource | We define a simple method to detect cortical states that can be applied in real time for offline processing of large amounts of recorded data on conventional computers. Also, the online detection of up and down states will facilitate the study of cortical dynamics. An open-source MATLAB toolbox, and Spike 2-compatible version are made freely available. Intracellular recordings from different areas of the cerebral cortex were obtained from both in vitro and in vivo preparations during slow oscillations. A method that separates up and down states recorded intracellularly is defined and analyzed here. The method exploits the crossover of moving averages, such that transitions between up and down membrane regimes can be anticipated based on recent and past voltage dynamics. We demonstrate experimentally the utility and performance of this method both offline and online, the online use allowing to trigger stimulation or other events in the desired period of the rhythm. This technique is compared with a histogram-based approach that separates the states by establishing one or two discriminating membrane potential levels. The robustness of the method presented here is tested on data that departs from highly regular alternating up and down states. The neuronal cortical network generates slow (<1 Hz) spontaneous rhythmic activity that emerges from the recurrent connectivity. This activity occurs during slow wave sleep or anesthesia and also in cortical slices, consisting of alternating up (active, depolarized) and down (silent, hyperpolarized) states. The search for the underlying mechanisms and the possibility of analyzing network dynamics in vitro has been subject of numerous studies. This exposes the need for a detailed quantitative analysis of the membrane fluctuating behavior and computerized tools to automatically characterize the occurrence of up and down states. | electrophysiology, intracellular recording, cortical state, real time, matlab, spike2, cerebral cortex | has parent organization: University of Malaga; Andalusia; Spain | Programa de Perfeccionamiento de Doctores of the Junta de Andaluca ; Ministry of Education and Science - Spain |
PMID:17849017 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30603 | SCR_003175 | 2026-08-15 11:22:27 | 1 | ||||||
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MAP Software Resource Report Resource Website 10+ mentions |
MAP Software (RRID:SCR_003170) | MAP Software | data processing software, software application, commercial organization, software resource | A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP Control Computer with the purchase of any MAP System. As the MAP System has been replaced by the advanced OmniPlex D Neural Data Acquisition System, Plexon is no longer developing the RASPUTIN software program. | electrophysiology, analysis, sort client, map server, spike sorting, windows | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000185 | SCR_003170 | Multichannel Acquisition Processor Software, RASPUTIN, Real-Time Acquisition System Programs for Unit Timing in Neuroscience, Real-Time Acquisition System Programs for Unit Timing in Neuroscience software | 2026-08-15 11:22:25 | 21 | ||||||||
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QDNAseq Resource Report Resource Website 100+ mentions |
QDNAseq (RRID:SCR_003174) | software resource | Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively. | software package, unix/linux, mac os x, windows, r, copy number variation, dna-seq, genetics, genome annotation, preprocessing, quality control, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25236618 | Free, Available for download, Freely available | OMICS_05902, biotools:qdnaseq | https://github.com/ccagc/QDNAseq, https://bio.tools/qdnaseq | SCR_003174 | QDNAseq - Quantitative DNA sequencing for chromosomal aberrations | 2026-08-15 11:22:25 | 168 | ||||||
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HuGE Navigator - Human Genome Epidemiology Navigator Resource Report Resource Website 100+ mentions |
HuGE Navigator - Human Genome Epidemiology Navigator (RRID:SCR_003172) | HuGE Navigator | data computation service, data or information resource, bibliography, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed. | environment, epidemiology, gene, genetic, genetic associations, genetic markers, genome, disease, human, human disease, predictive value, prevalence, publications, risk factors, test evaluations, variance, FASEB list |
has parent organization: Centers for Disease Control and Prevention works with: Kinase Associated Neural Phospho Signaling |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00573 | http://hugenavigator.net/HuGENavigator/home.do | SCR_003172 | 2026-08-15 11:22:25 | 117 | |||||||
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NGSadmix Resource Report Resource Website 100+ mentions |
NGSadmix (RRID:SCR_003208) | NGSadmix | software resource | A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program. | next generation sequencing, admixture proportion, admixture, genotype, c, c++, admixture, association study, population structure, resequencing |
is listed by: OMICtools has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:24026093 | Acknowledgement requested | OMICS_01553 | SCR_003208 | 2026-08-15 11:22:28 | 144 | |||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | simulation software, data processing software, software application, data analysis software, source code, software resource | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-08-15 11:22:26 | 129 | |||
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PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-08-15 11:22:28 | 69 |
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