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modMine: flexible access to modENCODE data.

Nucleic acids research | Jan 23, 2012

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine.

Pubmed ID: 22080565 RIS Download

Mesh terms: Animals | Caenorhabditis elegans | Databases, Genetic | Drosophila melanogaster | Gene Expression | Genome, Helminth | Genome, Insect | Genomics | Internet | User-Computer Interface

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This is a list of tools and resources that we have found mentioned in this publication.


MitoMiner

A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.

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Comprehensive Perl Archive Network

Welcome to CPAN, where you you will find All Things Perl. CPAN is the Comprehensive Perl Archive Network, a large collection of Perl software and documentation. You can begin exploring from either http://www.cpan.org/, http://www.perl.com/CPAN/ or any of the mirrors listed at http://www.cpan.org/SITES.html. Note that CPAN is also the name of a Perl module, CPAN.pm, which is used to download and install Perl software from the CPAN archive. This FAQ covers only a little about the CPAN module and you may find the documentation for it by using perldoc CPAN via the command line or on the web at http://search.cpan.org/dist/CPAN/lib/CPAN.pm. Sponsors: CPAN works with the generosity and cooperation of hundreds of developers, over 100 participating mirrors, funet.fi donating the network bandwidth, storage space and computing power, volunteers who help keep everything together and users whose interest in Perl keep the archive alive and growing. Keywords: Comprehension, Perl, Archive, Software, Documentation,

tool

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HMS Drosophila RNAi Screening Center

Core facility that provides the following services: Drosophila genome-wide and focused cell-based RNAi libraries, Custom synthesis of double-stranded RNAs for Drosophila cell-based RNAi.

The DRSC facilitates genome-wide and related cell-based screening at our state-of-the-art facility. Since our beginnings in 2003, we have successfully guided screeners through the process, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. Screens performed at the DRSC have resulted in an impressive number of publications on a wide range of topics in high-profile journals.

tool

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