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on page 1 showing 20 out of 43 results

Cite this (Assembly/Alignment/Annotation of 12 Related Drosophila Species, RRID:SCR_002921)

URL: http://rana.lbl.gov/drosophila

Resource Type: Resource, data set, topical portal, data or information resource, portal, organism-related portal

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

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Cite this (Berkeley Drosophila Genome Project, RRID:SCR_013094)

URL: http://www.fruitfly.org

Resource Type: Resource, topical portal, production service resource, analysis service resource, database, data analysis service, narrative resource, experimental protocol, portal, service resource, material resource, data or information resource

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

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    BestGene

Cite this (BestGene, RRID:SCR_012605)

URL: http://www.scienceexchange.com/facilities/bestgene-inc

Resource Type: Resource, service resource, commercial organization, core facility, access service resource

We provide high quality Drosophila transgenic service to both research institutions and companies. We offer you partial to full service ranging from DNA preparation, embryo microinjection, screening for white+, yellow+, and/or GFP/RFP phenotypes, to balancing crosses. Most importantly, the cost of our Drosophila embryo injection services is more reasonable compared to that of others. With a large number of facilities and the highly experienced staff, we are able to initiate the process immediately upon receiving your sample. Our friendly web-based database allows you to track your sample status, service history and more.

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Cite this (Centroid Trajectory Analysis, RRID:SCR_006331)

URL: http://buridan.sourceforge.net/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.

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    Clocklab

Cite this (Clocklab, RRID:SCR_014309)

URL: http://actimetrics.com/products/clocklab/

Resource Type: Resource, standalone software, data processing software, software application, data analysis software, software resource, data acquisition software

Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program.

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Cite this (Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays, RRID:SCR_001697)

URL: http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays

Resource Type: Resource, bibliography, data or information resource

A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

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    CRCView

Cite this (CRCView, RRID:SCR_007092)

URL: http://crcview.hegroup.org/

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

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.

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    Cscan

Cite this (Cscan, RRID:SCR_006756)

URL: http://159.149.160.51/cscan/

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

Data resource that includes a large collection of genome-wide ChIP-Seq experiments performed on transcription factors (TFs), histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes' loci. The input can be a cluster of co-expressed genes, or any other set of genes sharing a common regulatory profile. Users can thus single out which TFs are likely to be common regulators of the genes, and their respective correlations. Also, by examining results on promoter activation, transcription, histone modifications, polymerase binding and so on, users can investigate the effect of the TFs (activation or repression of transcription) as well as of the cell or tissue specificity of the genes' regulation and expression.

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Cite this (DroID - Drosophila Interactions Database, RRID:SCR_006634)

URL: http://www.droidb.org

Resource Type: Resource, data or information resource, database

A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available.

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Cite this (Drosophila polymorphism database, RRID:SCR_007629)

URL: http://dpdb.uab.es

Resource Type: Resource, data or information resource, database

Database providing a collection of all the existing polymorphic sequences in the Drosophila genus. It allows users to search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is updated daily and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing.

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Cite this (ESTHER DateBase, RRID:SCR_008479)

URL: http://bioweb.ensam.inra.fr/esther

Resource Type: Resource, data or information resource, database

Database and tools for the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases. ESTHER stands for ESTerases and alpha/beta Hydrolase Enzymes and Relatives. Covers multiple species, including human, mouse caenorhabditis and drosophila.

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Cite this (Evolutionary Rate Covariation, RRID:SCR_015669)

URL: http://csb.pitt.edu/erc_analysis/Methods.php

Resource Type: Resource, software resource, software application, data analysis software, data processing software, web application

Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.

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Cite this (Flannotator, RRID:SCR_001608)

URL: http://www.flyprot.org/

Resource Type: Resource, data or information resource, database

Allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabulary to ensure data integrity.

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    FlyBase

Cite this (FlyBase, RRID:SCR_006549)

URL: http://flybase.org/

Resource Type: Resource, topical portal, organism-related portal, analysis service resource, database, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resource

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

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Cite this (Flybrain at Stanford, RRID:SCR_001877)

URL: http://flybrain.stanford.edu/

Resource Type: Resource, image analysis software, data processing software, software application, image collection, software resource, data or information resource

Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.

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    Fly EM

Cite this (Fly EM, RRID:SCR_002242)

URL: http://www.janelia.org/team-project/fly-em

Resource Type: Resource, segmentation software, image analysis software, topical portal, data processing software, software application, data set, portal, software resource, data or information resource

A project producing datasets, software, and algorithms that is developing the technology to produce connectomes at the electron microscopic level of behaviorally-relevant neural circuits as well as the entire Drosophila nervous system. This technology will enable them to create a map of every neuron and synapse in the Drosophila nervous system, using novel approaches to electron microscopy (EM) as the foundation. In the same way that the fly genome paved the way for larger projects, including sequencing the human genome, Fly EM may ultimately contribute to our understanding of the human brain by establishing a fly "connectome" a map that shows how all neurons in the fly brain are connected to each other. They began their entry into EM reconstruction with the fly's adult visual system, where much is known about cell types from previous EM and histological studies, as well as ongoing studies in the Fly Light Project. In addition to establishing and publishing a fly connectome, Fly EM will make technology and methodology available that is needed to perform large-scale EM reconstructions. Fly EM will generally pursue an open policy with their datasets, software, and algorithms after relevant publications. When an EM reconstruction is published, the derived connectome and reconstructed neuronal skeletons will be made available online. The raw data and annotatations will be made available upon request as logistics dictate. To encourage further collaboration and scientific discovery, a small fraction of their raw data and corresponding segmentation will be made available independent of publication. Their goal is to enable others who wish to approach the many algorithmic challenges, but who do not have access to an EM facility, to have the data they need to support methods development, as well as their results to use as a benchmark. Fly EM emphasizes publication of supporting techniques and software approaches before major EM reconstruction releases to encourage rapid feedback from the community and adoption of their strategies. FlyEM maintains much of its software in the open-source repository GitHub:http://janelia-flyem.github.com. They will provide information on official release versions of these packages on git-hub when it reaches reasonable maturity.

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    FlyMine

Cite this (FlyMine, RRID:SCR_002694)

URL: http://www.flymine.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

An integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

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    flytrap

Cite this (flytrap, RRID:SCR_003075)

URL: http://www.fly-trap.org/

Resource Type: Resource, image, data or information resource, video resource, database

Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.

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    Gemma

Cite this (Gemma, RRID:SCR_008007)

URL: http://www.chibi.ubc.ca/Gemma

Resource Type: Resource, data or information resource, database

Database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.

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Cite this (GeneNetwork, RRID:SCR_002388)

URL: http://www.genenetwork.org/

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

A group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. It combines more than 25 years of legacy data generated by hundreds of scientists together with sequence data (SNPs) and massive transcriptome data sets (expression genetic or eQTL data sets). The quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Most of these population data sets are linked with dense genetic maps (genotypes) that can be used to locate the genetic modifiers that cause differences in expression and phenotypes, including disease susceptibility. Users are welcome to enter their own private data directly into GeneNetwork to exploit the full range of analytic tools and to map modulators in a powerful environment. This combination of data and fast analytic functions enable users to study relations between sequence variants, molecular networks, and function. What can be done with GeneNetwork? * QTL Mapping: ** Interval Mapping ** Simple interval mapping ** Composite interval mapping ** Pair-scan * Correlation Analysis ** Correlation Matrix / Principal Components Analysis ** QTL Heatmaps ** Compare Correlates ** Network Graph * Systems Genetics and Complex Trait Analysis Source code is available and is written in Python, C, and JavaScript. The QTL Reaper module of GeneNetwork that is used by several mapping modules of GeneNetwork is also available.

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