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Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways.
Proper citation: MetaNetX (RRID:SCR_015882) Copy
Open community of researchers, educators, and professionals with goal of improving way we develop, share, use, and re-use agent based and computational models for study of social and ecological systems. Develops and maintains CoMSES Model Library, digital repository that supports discovery and good practices for software citation, digital preservation, reproducibility, and reuse.
Proper citation: CoMSES Net (RRID:SCR_017598) Copy
Services for the long-term preservation and curation of America's digital data - data of any type or size, with minimal requirements on the data provider. It has the capacity to preserve hundreds of terabytes of digital data and comprises several partner organizations that provide a wide range of services. The project leverages high-speed networks, mass-scale storage capabilities, and the expertise of the partners in order to provide a geographically distributed, heterogeneous, and highly redundant archive system. Features of the project include: * Three geographically distributed copies of the data * Curatorial audit reporting * Development of best practices for data packaging and sharing Chronopolis is available to anyone who wants to have their data preserved. Storage is based on a yearly, per-terabyte charge. The smallest unit available is one terabyte; collections smaller than this will be charged the one terabyte rate.
Proper citation: chronopolis (RRID:SCR_003116) Copy
https://github.com/di-0579/spatial_tri-omics
Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.
Proper citation: spatial_tri-omics (RRID:SCR_026194) Copy
Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.
Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.
Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy
http://pubchem.ncbi.nlm.nih.gov/
Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).
Proper citation: PubChem (RRID:SCR_004284) Copy
EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.
Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy
http://physionet.org/physiobank/
Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them.
Proper citation: Physiobank (RRID:SCR_006949) Copy
https://github.com/HussainiLab/hfoGUI
Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony.
Proper citation: hfoGUI (RRID:SCR_016726) Copy
http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage
System designed for automated collection of images from a transmission electron microscope.
Proper citation: Leginon (RRID:SCR_016731) Copy
https://icsd.products.fiz-karlsruhe.de/
Database for completely identified inorganic crystal structures. Collection of known inorganic crystal structures published since 1913, including their atomic coordinates. Includes only data which have passed thorough quality checks. Tool for materials research.
Proper citation: Inorganic Crystal Structure Database (ICSD) (RRID:SCR_017429) Copy
Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com.
Proper citation: NIH Figshare Archive (RRID:SCR_017580) Copy
https://ki.se/en/research/the-swedish-twin-registry
Registry contains information about twin pairs for which zygosity is known, both mono- and dizygotic pairs. Registry covers older, middle, and younger cohorts. There are approximately 30 projects ongoing based on data from this registry.
Proper citation: Swedish Twin Registry (RRID:SCR_017478) Copy
https://clowder.ncsa.illinois.edu/
Web based data management system that allows users to share, annotate, organize and analyze large collections of datasets. Software tool for creating some metadata about software tools automatically. Open source data management for long tail data. Provides support for extensible metadata annotation and distributed analytics for automatic curation of uploaded data. Open source software that can be customized and deployed on your own cloud.
Proper citation: Clowder (RRID:SCR_017599) Copy
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/
Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released.
Proper citation: SARS-CoV-2-Sequences (RRID:SCR_018319) Copy
https://amp.pharm.mssm.edu/covid19/
Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.
Proper citation: COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) Copy
Database for study of early phonological development using Phon program. Child phonology component of TalkBank system.
Proper citation: PhonBank (RRID:SCR_016312) Copy
https://www.ebi.ac.uk/metagenomics/
Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.
Proper citation: MGnify (RRID:SCR_016429) Copy
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