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Found 50 result(s)

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.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

National Omics Data Encyclopedia

NODE

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NODE (The National Omics Data Encyclopedia) provides an integrated, compatible, comparable, and scalable multi-omics resource platform that supports flexible data management and effective data release. NODE uses a hierarchical data architecture to support storage of muti-omics data including sequencing data, MS based proteomics data, MS or NMR based metabolomics data, and fluorescence imaging data. Launched in early 2017, NODE has collected and published over 900 terabytes of omics data for researchers from China and all over the world in last three years, 22% of which contains multiple omics data. NODE provides functions around the whole life cycle of omics data, from data archive, data requests/responses to data sharing, data analysis, data review and publish.

National Genomics Data Center

国家基因组科学数据中心

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The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), advances life & health sciences by providing open access to a suite of resources, with the aim to translate big data into big discoveries and support worldwide activities in both academia and industry.

China National GeneBank DataBase

国家基因库生命大数据平台

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The China National GeneBank database (CNGBdb) is a unified platform for biological big data sharing and application services. CNGBdb has now integrated a large amount of internal and external biological data from resources such as CNGB, NCBI, and the EBI. There are several sub-databases in CNGBdb, including literature, variation, gene, genome, protein, sequence, organism, project, sample, experiment, run, and assembly. Based on underlying big data and cloud computing technologies, it provides various data services, including archive, analysis, knowledge search, and management authorization of biological data. CNGBdb adopts data structures and standards of international omics, health, and medicine, such as The International Nucleotide Sequence Database Collaboration (INSDC), The Global Alliance for Genomics and Health GA4GH (GA4GH), Global Genome Biodiversity Network (GGBN), American College of Medical Genetics and Genomics (ACMG), and constructs standardized data and structures with wide compatibility. All public data and services provided by CNGBdb are freely available to all users worldwide. CNGB Sequence Archive (CNSA) is the bionomics data repository of CNGBdb. CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in life science, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, and Sequence. Moreover, CNSA has achieved the correlation of sample entities, sample information, and analyzed data on some projects. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.CNGB Sequence Archive (CNSA) is a convenient and efficient archiving system of multi-omics data in the life science of CNGBdb, which provides archiving services for raw sequencing reads and further analyzed results. CNSA follows the international data standards for omics data, and supports online and batch submission of multiple data types such as Project, Sample, Experiment/Run, Assembly, Variation, Metabolism, Single cell, Sequence. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing.

Antimicrobial Peptide Database

APD

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The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade.

Biofilm-active AMPs database

BaAMPs

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BaAMPs is the first database dedicated to antimicrobial peptides (AMPs) specifically tested against microbial biofilms. The aim of this project is to provide useful resources for the study of AMPs against biofilms to microbiologist, bioinformatics researcher and medical scientist working in this field in an open-access framework.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

Carbohydrate Structure Database

CSDB

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This is CSDB version 1 merged from Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases. This database aims at provision of structural, bibliographic, taxonomic, NMR spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. It has been merged from the Bacterial and Plant&Fungal Carbohydrate Structure Databases (BCSDB+PFCSDB). The key points of this service are: High coverage. The coverage for bacteria (up to 2016) and archaea (up to 2016) is above 80%. Similar coverage for plants and fungi is expected in the future. The database is close to complete up to 1998 for plants, and up to 2006 for fungi. Data quality. High data quality is achieved by manual curation using original publications which is assisted by multiple automatic procedures for error control. Errors present in publications are reported and corrected, when possible. Data from other databases are verified on import. Detailed annotations. Structural data are supplied with extended bibliography, assigned NMR spectra, taxon identification including strains and serogroups, and other information if available in the original publication. Services. CSDB serves as a platform for a number of computational services tuned for glycobiology, such as NMR simulation, automated structure elucidation, taxon clustering, 3D molecular modeling, statistical processing of data etc. Integration. CSDB is cross-linked to other glycoinformatics projects and NCBI databases. The data are exportable in various formats, including most widespread encoding schemes and records using GlycoRDF ontology. Free web access. Users can access the database for free via its web interface (see Help). The main source of data is retrospective literature analysis. About 20% of data were imported from CCSD (Carbbank, University of Georgia, Athens; structures published before 1996) with subsequent manual curation and approval. The current coverage is displayed in red on the top of the left menu. The time lag between the publication of new data and their deposition into CSDB is ca. 1 year. In the scope of bacterial carbohydrates, CSDB covers nearly all structures of this origin published up to 2016. Prokaryotic, plant and fungal means that a glycan was found in the organism(s) belonging to these taxonomic domains or was obtained by modification of those found in them. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds in which at least one residue is a sugar or its derivative.

Small Molecule Pathway Database

formerly: PathBank

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The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

IMGT/mAb-DB

ImMunoGeneTics/MAB-DB

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IMGT/mAb-DB provides a unique expertised resource on monoclonal antibodies (mAbs) with diagnostic or therapeutic indications, fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA) and relative proteins of the immune system (RPI) with clinical indications.

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB

International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB

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IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

IMGT/PRIMER-DB

International ImMunoGeneTics information system/PRIMER-Database

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The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).

IMGT/LIGM-DBI

International ImMunoGeneTics information system / Laboratoire d'ImmunoGénétique Moléculaire-Database

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IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

EchoBase

an integrated post-genomic database for E.coli

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EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

Pathogen Portal

the Bioinformatics Resource Centers Portal

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Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. The Pathogen Portal supports and links to five Bioinformatics Resource Centers (BRCs). Each BRC specializes in a different group of pathogens, focusing on, but not limited to, pathogens causing (Re-)Emerging Infectious Diseases, and those in the NIAID Category A-C Priority Pathogen lists for biodefense research. The scope of the BRCs also includes Invertebrate Vectors of Human Disease. Pathogen Portal covers EuPathDB, IRD, PATRIC, VectorBase and ViPR.

Virus Pathogen Resource

ViPR

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Migration of the data, tools, and services from IRD and ViPR to BV-BRC is complete! We are now in the sunsetting phase of the transition. Starting on October 31, 2022, launching the IRD or ViPR home pages will redirect you to the new BV-BRC home page. The current plan is to completely shut down IRD and ViPR by the end of this calendar year. Although it will still be possible to use those sites until shutdown, we strongly encourage you to start using BV-BRC now.

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Synapse

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Synapse is an open source software platform that clinical and biological data scientists can use to carry out, track, and communicate their research in real time. Synapse enables co-location of scientific content (data, code, results) and narrative descriptions of that work.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

The Taenia solium Genome Project

T. solium Genome Project

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>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

German Federation for Biological Data

GFBio

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The project brings together national key players providing environmentally related biological data and services to develop the ‘German Federation for Biological Data' (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research.

Influenza Research Database

IRD

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<<<!!!<<< The migration of the data, tools, and services from the legacy IRD and ViPR applications to BV-BRC is now complete. All web traffic from the IRD and ViPR resources is also being forwarded to the BV-BRC home page https://www.re3data.org/repository/r3d100014100 >>>!!!>>>

MetaboLights

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MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments.