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MetaSRA / Meta Sequence Read Archive
A database of normalized sequence read archive (SRA) sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. MetaSRA involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. This tool is comprised of three parts: (i) Sample labels, using terms from the following biomedical ontologies (Disease Ontology, Cell Ontology, Uberon, Experimental Factor Ontology and the Cellosaurus); (ii) A sample-type classification, with six sample-type categories similar to those used by ENCODE; (iii) Standardized numerical properties of the sample.
VaProS / VAriation effect on PROtein Structure and function
Integrates information in structural biology with genome, transcriptome, interactome and other information and provides seamless environment to scientists for analyzing these different types of information derived from different databases. The developers of VaProS aim to establish a core technology for drug discovery and other related fields in this country by providing a bird's-eye view of the whole data that assists a hypothesis (model) building process and by providing information manipulation environment that enables problem solving toward drug discovery and other related fields. VaProS is going to realize the aims above by integrating and disseminating the outcomes of the national projects in the related fields in the past to both structural biology and the whole life science discipline of not only academia, but industrial world as well.
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BioSD / BioSamples Database
A database at EBI that stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i) recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; (ii) minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and (iii) supporting cross database queries by sample characteristics. Each sample in the database is assigned an accession number. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers.
TIARA / Total Integrated Archive of short-Read and Array
Gathers information about raw-level personal genomic data from whole genome next generation sequencing (NGS) and ultra-high-resolution comparative genomic hybridization (CGH) arrays. TIARA enables detection of personal genomic variations, such as single nucleotide polymorphisms (SNPs), short insertions/deletions (indels), and structural variants (SVs). Moreover, the database also provides deposits of sequencing reads for 13 whole genomes and 16 transcriptomes at high depth of coverage from high-throughput sequencing machines including the Illumina Genome Analyzer and AB SOLiD.
Congregates computational neuroscience models in any simulator format or programming language. ModelDB provides a free platform, both public and private, which allows users to submit the source code form associated with a published model. The repository includes over 1000 models displayed into more than 130 topics. The database includes several functionalities, such as ModelView to examine run-time morphology, channel types, and values of parameters, or an advanced search mode allowing searching according to sixteen parameters.
Facilitates the capture and management of structured metadata and data for diverse biological research projects. BioProject constitutes an online resource to describe a project’s scope and objectives. The metadata collected includes structured information about the type of research investigation as genome sequencing and gene expression, project title and goals, the submitting group, environmental sample label or organism and some project data type attributes regarding the sample scope, target and method.
Permits efficient searching of its database containing comprehensive information for all public RNA-seq data sets on mice with genotype as a factor. RNASeqMetaDB contains metadata for a total of 306 experiments targeting 298 different genes. Users can search the database using multiple parameters like genes, diseases, tissue types, keywords, and associated publications in order to find data sets that match their interests. Summary statistics of the metadata is also presented on the web server showing interesting global patterns of RNA-Seq studies.
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