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Found 92 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.

AlphaFold

AlphaFold Protein Structure Database

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AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.

Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

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The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.

FaceBase

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FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.

Broad GDAC Firehose

Genome Data Analysis Center

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Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month. More information: https://broadinstitute.atlassian.net/wiki/spaces/GDAC/

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.

ArachnoServer

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ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. Spiders are the largest group of venomous animals and they are predicted to contain by far the largest number of pharmacologically active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built so that a wide range of biological scientists, including neuroscientists, pharmacologists, and toxinologists, can readily access key data relevant to their discipline without being overwhelmed by extraneous information.

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.

Progenetix

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The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32548 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1031 articles and represents 366 different cancer types, according to the International classification of Diseases in Oncology (ICD-O).

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.

ALSoD

ALS Online Database

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ALSoD is a freely available database that has been transformed from a single gene storage facility recording mutations in the SOD1 gene to a multigene ALS bioinformatics repository and analytical instrument combining genotype, phenotype, and geographical information with associated analysis tools. These include a comparison tool to evaluate genes side by side or jointly with user configurable features, a pathogenicity prediction tool using a combination of computational approaches to distinguish variants with nonfunctional characteristics from disease-associated mutations with more dangerous consequences, and a credibility tool to enable ALS researchers to objectively assess the evidence for gene causation in ALS. Furthermore, integration of external tools, systems for feedback, annotation by users, and two-way links to collaborators hosting complementary databases further enhance the functionality of ALSoD.

Health Atlas

Leipzig Health Atlas

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The Health Atlas is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research projects from the partner institutions.

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.

SimTK

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SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects. It has over 126.656 members, hosts 1.648 projects from researchers around the world, and has had more than 2.095.783 files downloaded from it. Individuals have created SimTK projects to meet publisher and funding agencies’ software and data sharing requirements, run scientific challenges, create a collection of their community’s resources, and much more.

OMICtools

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>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. While we made tremendous progress over the past three years, developing a bioinformatics database of software and dynamic protocols, attracting more than 1.5M visitors a year, we lacked the financial support we needed to continue. We certainly gave it our all. We'd like to thank everyone who believed in us and supported us on this journey: all our users, our community, our friends, families and employees (who we consider as our extended family!). omicX will probably shut down its operations within the next few weeks. The team and I remain firmly committed to our vision, particularly at this very difficult time. It is now, more than ever before, that researchers need access to a resource that pools collective scientific intelligence. We have accumulated an awful lot of experience which we are keen to share. If your institution would be interested in taking over our website and database, to provide researchers with continued access to the platform, or you simply want to stay in touch with the omicX team, contact us at contact@omictools.com or at carine.toutain@fhbx.eu.