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on page 1 showing 20 out of 53 results

Cite this (AnimalTFDB, RRID:SCR_001624)

URL: http://www.bioguo.org/AnimalTFDB/

Resource Type: Resource, data or information resource, database

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.

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    ARACNE

Cite this (ARACNE, RRID:SCR_002180)

URL: http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE

Resource Type: Resource, software resource, software application

An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

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Cite this (Atlas of Living Australia, RRID:SCR_006467)

URL: http://www.ala.org.au/

Resource Type: Resource, database, service resource, storage service resource, software resource, image repository, data repository, data or information resource

Repository of scientifically collected data on all the known species in Australia aggregated from a wide range of data providers: museums, herbaria, community groups, government departments, individuals and universities. Data records consist of images, literature, molecular DNA data, identification keys, species interaction data, species profile data, nomenclature, source data, conservation indicators, and spatial data. Several standards are preferred for data provided to the Atlas. Use this site to: * access information pages for each species containing photos, descriptions, maps and observations * access scientific and common names * explore the flora and fauna reported around your neighborhood * learn about Australia's biodiversity collections at museums, herbaria and other institutions * learn about citizen science projects * map, analyze and visualize biodiversity and environmental data and trends * access tools to help track changes in biodiversity and the environment * download and use open source tools * download biodiversity data * access images, literature and genetic information through Australian nodes of international data repositories * volunteer for digitization projects. The Atlas of Living Australia (Atlas) and its associated information systems provides web services for accessing information over the internet.

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    BioCyc

Cite this (BioCyc, RRID:SCR_002298)

URL: http://biocyc.org/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.

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    BioRep

Cite this (BioRep, RRID:SCR_004907)

URL: http://www.biorep.it/en

Resource Type: Resource, material analysis service, analysis service resource, biomaterial supply resource, biospecimen repository, production service resource, tissue bank, material service resource, service resource, storage service resource, cell repository, biomaterial analysis service, material resource, biomaterial manufacture, material storage repository

Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

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Cite this (Blue Brain Project, RRID:SCR_002994)

URL: http://bluebrain.epfl.ch/

Resource Type: Resource, topical portal, portal, data or information resource

A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.

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Cite this (Brad Smith Magnetic Resonance Imaging of Embryos, RRID:SCR_006300)

URL: http://www-personal.umich.edu/~brdsmith/Research.html

Resource Type: Resource, data set, video resource, image collection, data or information resource

Data set of image collections and movies including Magnetic Resonance Imaging of Embryos, Human Embryo Imaging, MRI of Cardiovascular Development, and Live Embryo Imaging. Individual MRI slice images, three-dimensional images, animations, stereo-pair animations, animations of organ systems, and photo-micrographs are included.

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Cite this (BraInSitu: A homepage for molecular neuroanatomy, RRID:SCR_008081)

URL: http://www.nibb.ac.jp/brish/indexE.html

Resource Type: Resource, database, image, expression atlas, narrative resource, experimental protocol, atlas, data or information resource

Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE.

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    canSAR

Cite this (canSAR, RRID:SCR_006794)

URL: https://cansar.icr.ac.uk/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data.

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Cite this (Cell Type Ontology, RRID:SCR_004251)

URL: http://cellontology.org

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

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    ChEA

Cite this (ChEA, RRID:SCR_005403)

URL: http://amp.pharm.mssm.edu/lib/chea.jsp

Resource Type: Resource, data analysis service, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resource

Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes.

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Cite this (Common Upper Mammalian Brain Ontology, RRID:SCR_003629)

URL: http://www.incf.org/activities/our-programs/pons/cumbo

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology of formal definitions (i.e., machine processable) for the types of structures commonly described in neuroanatomy.

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    CORUM

Cite this (CORUM, RRID:SCR_002254)

URL: http://mips.helmholtz-muenchen.de/genre/proj/corum

Resource Type: Resource, data or information resource, database

Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded.
The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%).

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Cite this (CSHL - Hannon Lab, RRID:SCR_005982)

URL: http://hannonlab.cshl.edu/index.html

Resource Type: Resource, laboratory portal, portal, organization portal, data or information resource

The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution.

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    ERANGE

Cite this (ERANGE, RRID:SCR_005240)

URL: http://woldlab.caltech.edu/rnaseq

Resource Type: Resource, software resource

Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.

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    FEED

Cite this (FEED, RRID:SCR_000637)

URL: http://www.feedexp.org/

Resource Type: Resource, software resource, source code, data or information resource, database

Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

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    GeneSeer

Cite this (GeneSeer, RRID:SCR_002626)

URL: http://geneseer.com/

Resource Type: Resource, data or information resource, database

Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans.

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Cite this ( Globin Gene Server , RRID:SCR_001480)

URL: http://globin.cse.psu.edu/

Resource Type: Resource, source code, data analysis service, resource, database, analysis service resource, production service resource, narrative resource, service resource, training material, software resource, data or information resource

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

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    GOblet

Cite this (GOblet, RRID:SCR_006998)

URL: http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms.

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Cite this (G:Profiler, RRID:SCR_006809)

URL: http://biit.cs.ut.ee/gprofiler/

Resource Type: Resource, analysis service resource, software resource, data analysis service, service resource, production service resource

A web-based toolset for functional profiling of gene lists from large-scale experiments. It has a simple web interface with powerful visualization. It currently supports 85 species, including mammals, fungi, plants, insects, etc, from the Ensembl and Ensembl Genomes databases. g:Profiler consists of the following tools: * g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualization of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results. * g:Convert allows conversion between gene or protein names, database IDs and microarray probes of more than 100 types. A mix of various IDs may be presented as input; output options include HTML, text and XLS spreadsheet. * g:Orth retrieves orthologs for a given set of genes, proteins or probes in a selected organism. Graphical representation also shows orthologs present in all g:Profiler organisms. * g:Sorter searches for similar expression profiles to a given gene, protein or probe in a large set of public microarray datasets from the Gene Expression Omnibus (GEO) database. * g:Cocoa provides a compact interface for comparing enrichments of multiple gene lists. Platform: Online tool

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