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Found 39 result(s)

The Cell Image Library

The Cell

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This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The Cell Image Library has been merged with "Cell Centered Database" in 2017. The purpose of the database is to advance research on cellular activity, with the ultimate goal of improving human health.

NCBI PopSet

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NCBI PopSet collects DNA sequences to analyze the ways that populations are related by evolution. Such sequences indicate if populations originate from different members of the same species or from organisms of different species entirely.

NCBI Nucleotide

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The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.

Pseudobase

A Pseudoknot Database

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Since the first discovery of RNA pseudoknots more and many more pseudoknots have been found. However, not all of those pseudoknot data are easy to trace. Sometimes the information is hidden in a publication where the title gives no hint that pseudoknot information is there. This was the first reason that we thought that a general accessible information source for pseudoknots would be handy.

SWISS-MODEL Repository

SMR

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The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

Protein Lysine Modification Database

PLMD

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PLMD (Protein Lysine Modifications Database) is an online data resource specifically designed for protein lysine modifications (PLMs). The PLMD 3.0 database was extended and adapted from CPLA 1.0 (Compendium of Protein Lysine Acetylation) database and CPLM 2.0 (Compendium of Protein Lysine Modifications) database

MiCroKitS

formerly: MiCroKit

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During cell cycle, numerous proteins temporally and spatially localized in distinct sub-cellular regions including centrosome (spindle pole in budding yeast), kinetochore/centromere, cleavage furrow/midbody (related or homolog structures in plants and budding yeast called as phragmoplast and bud neck, respectively), telomere and spindle spatially and temporally. These sub-cellular regions play important roles in various biological processes. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens based on the rationale of "Seeing is believing" (Bloom K et al., 2005). Through ortholog searches, the proteins potentially localized at these sub-cellular regions were detected in 144 eukaryotes. Then the integrated and searchable database MiCroKiTS - Midbody, Centrosome, Kinetochore, Telomere and Spindle has been established.

Genome Sequence Archive

GSA

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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

RIKEN Bioresource Research Center

RIKEN BRC

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Bioresources, often referred to as biological resources, are essential experimental research materials for life science and bioindustry. Under the three principles of “Trust”, “Sustainability” and “Leadership”, RIKEN BRC is committed to receiving deposition/donation of bioresources from the research community, confirming the authenticity of bioresources by rigorous quality examination, preserving, and distributing them back to the research community. f you wish to search quickly or to search multiple bioresources (mouse, cell, plant, microorganism, gene) simultaneously, we recommend to search from the Top Page. At the Top page, bioresource search and Google-based site search are available.

Cotton Functional Genomics Database

CottonFGD

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Cotton Functional Genomics Database (CottonFGD) integrates with modern genomic/transcriptomic data and earch/analysis/visualization modules. It aims at providing an easy, quick and visualized data analysis platform for cotton (Gossypium spp) researchers and other functional genomic researches.

National Freshwater Genetic Resource Center

国家淡水水产种质资源库

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National freshwater aquatic germplasm repository, competent department: Ministry of Agriculture and Rural Affairs, relying unit: China Academy of Fisheries Science. By the Heilongjiang Fisheries Research Institute, Yangtze River Fisheries Research Institute, Freshwater Fisheries Research Center, Pearl River Fisheries Research Institute, Fisheries Machinery and Instruments Research Institute and Shanghai Ocean University 6 units. Relying on the unit's outstanding ability to informatization of resources, the establishment of an advanced system, functional, stable operation, high visibility in the field of portal, can carry out deep mining and digital processing of freshwater aquatic germplasm resources information. The co-construction unit has relatively complete functional laboratory, preservation library and base facilities, with the hardware conditions to provide knowledge-based and professional services of freshwater aquatic germplasm resources. The participants have many years of experience in the collection and integration of freshwater aquatic germplasm resources, with solid professional background and outstanding business ability, which can improve the depth and breadth of integration and utilization of freshwater aquatic germplasm resources.

AgBase

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AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models.

PMN

Plant Metabolic Network

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The Plant Metabolic Network (PMN) provides a broad network of plant metabolic pathway databases that contain curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism in plants. The PMN currently houses one multi-species reference database called PlantCyc and 22 species/taxon-specific databases.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.

The Global Proteome Machine

GPM

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The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.

Expression Atlas

Gene Expression Atlas

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The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displays information about which gene products are present (and at what abundance) in "normal" conditions (e.g. tissue, cell type). It aims to answer questions such as "which genes are specifically expressed in human kidney?". This component of the Expression Atlas consists of highly-curated and quality-checked RNA-seq experiments from ArrayExpress. It has data for many different animal and plant species. New experiments are added as they become available. The Differential Atlas allows users to identify genes that are up- or down-regulated in a wide variety of different experimental conditions such as yeast mutants, cadmium treated plants, cystic fibrosis or the effect on gene expression of mind-body practice. Both microarray and RNA-seq experiments are included in the Differential Atlas. Experiments are selected from ArrayExpress and groups of samples are manually identified for comparison e.g. those with wild type genotype compared to those with a gene knock out. Each experiment is processed through our in-house differential expression statistical analysis pipeline to identify genes with a high probability of differential expression.

GeneLab

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GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, and create collaborative projects using the Collaborative Workspace. GeneLab promises to facilitate and improve information sharing, foster innovation, and increase the pace of scientific discovery from extremely rare and valuable space biology experiments. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight. GeneLab helps scientists understand how the fundamental building blocks of life itself – DNA, RNA, proteins, and metabolites – change from exposure to microgravity, radiation, and other aspects of the space environment. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data alongside essential metadata describing each spaceflight and space-relevant experiment. By carefully curating and implementing best practices for data standards, users can combine individual GeneLab datasets to gain new, comprehensive insights about the effects of spaceflight on biology. In this way, GeneLab extends the scientific knowledge gained from each biological experiment conducted in space, allowing scientists from around the world to make novel discoveries and develop new hypotheses from these priceless data.

cropPAL

Compendium of crop Proteins with Annotated Locations

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<<<!!!<<<This repository is no longer available>>>!!!>>>

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

NCBI Protein Clusters

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The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.

National Parasite Resource Center

国家寄生虫资源库

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From 2005 to 2008, with the support of the Ministry of Science and Technology (MOST), the construction of parasite germplasm repositories has spread to 20 conservation institutions in 15 provinces (cities) nationwide, with 3 physical exhibition halls; 3 live parasite conservation centers. A total of 1115 species/117814 pieces of parasitic germplasm resources of 23 orders in 11 phyla have been integrated into the physical library and database, including human parasites and vectors, animal parasites, plant nematodes, medical insects, trematodes, and parasitic snails, and the resources are combined with moderate distribution, medium- and long-term support, and off-site duplicates. The number of resources accounts for 39.27% of the national total. Through 10 years of accumulation, we have built the largest and only parasite species resource database in the field of parasites in China, and created a sharing platform of parasite germplasm resource center.

NCBI Protein

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The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.

BioGRID ORCS

BioGRID Open Repository of CRISPR Screens

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BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. The current index is version 1.0.3 and searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines. All screen data are freely provided through our search index and available via download in a wide variety of standardized formats.

Array Express

functional genomics data

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ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

National Aquatic Biological Resource Center

国家水生生物种质资源库

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National Aquatic Biological Resource Center (NABRC), established in June 2019, is a member of National Science and Technology Resource Platform supported by the Ministry of Science and Technology and the Ministry of Finance. The NABRC consists of 6 sub-platforms. In summary, these six sub-platforms have reached leading levels at home and abroad in terms of the resource richness, the resource digitization, as well as the amount and quality of resource services. Right now, these platforms are in strong support of basic biology, basic medicine, aquatic economics, water environmental protection and other areas in China. It is an essential way to practice the "Great Yangtze River Protection" and promote the construction of ecological civilization in the Yangtze River. In the future, the platforms will further integrate different types of resources, optimize the resource configuration and improve the service systems, so as to build a high standard resource sharing platform on a global scale and promote international communication and cooperation.