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DuraSpace sustains and grows its flagship repository platforms--Fedora and DSpace--while expanding into new technologies. DuraSpace is the independent 501(c)(3) not-for-profit born from a vision to help save our shared scholarly, scientific and cultural record. We are dedicated to sustaining and improving Fedora and DSpace, two of the most dominant open source repository solutions. We continue to lead the development and improvement of open technologies that provide long-term, durable access to your digital assets. Our new technology, DuraCloud, will exploit digital preservation support services in the cloud. We are also expanding into new areas that include exploring strategies on how to manage the ''data deluge'' and addressing the challenge of converting the overwhelming amount of data produced by scholars and scientists into useful information. DuraSpace is committed to providing leadership and innovation in the development and deployment of open technologies that promote durable, persistent access to digital data. We collaborate with academic, scientific, cultural, and technology communities in creating practical solutions to help ensure that current and future generations have access to our collective digital heritage. Our values are expressed in our organizational byline, open technologies for durable digital content.
Proper citation: DuraSpace (RRID:SCR_005866) Copy
Publicly available repository of high throughput sequencing data. KRA stores qualified raw sequencing data and alignment information and facilitates reproducibility through cloud-based data analysis service. Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data has been migrated to KRA.
Proper citation: Korea Sequence Read Archive (RRID:SCR_028271) Copy
http://www.nitrc.org/projects/nitrc_es/
Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.
Proper citation: NITRC Enhanced Services (RRID:SCR_002494) Copy
List of proteins commonly found in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. List is based on analysis of current version of GPMDB, as well as suggestions by users. Current version of cRAP in FASTA format can be obtained from the GPM FTP site.
Proper citation: cRAP protein sequences (RRID:SCR_018187) Copy
https://repository.nced.umn.edu/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment.
Proper citation: National Center for Earth-Surface Dynamics (RRID:SCR_002195) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications.
Proper citation: iDASH (RRID:SCR_003524) Copy
Consortium to improve health outcomes and reduce HIV transmission among diverse range of populations affected by alcohol and HIV infection in Florida. Fosters interdisciplinary translational research, training and community engagement. One of five national Consortia for HIV/AIDS and Alcohol Research Translation (CHAART). Supports Researcher Hub for researchers interested in SHARC research, publication, presentations, and opportunity to access, and analyze datasets via SHARC Concepts System.
Proper citation: Southern HIV and Alcohol Research Consortium (RRID:SCR_023435) Copy
Web-based resource for preserving and sharing pharmacokinetic data generated through preclinical and clinical HIV research.
Proper citation: HIV Pharmacology (RRID:SCR_028109) Copy
https://array.nci.nih.gov/caarray/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.
Proper citation: caArray (RRID:SCR_006053) Copy
Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.
Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy
Supports oceanographic research by providing access to high quality, global, vessel-based CTD and hydrographic data from GO-SHIP, WOCE, CLIVAR and other repeat hydrography programs. These data are openly accessible and served in standardized community formats (WHP-Exchange, WOCE, and netCDF). CCHDO also manages public and non-public CTD data for use by the global Argo and OceanSITES programs.
Proper citation: CCHDO (RRID:SCR_007093) Copy
https://www.ebi.ac.uk/covid-19
EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
Proper citation: EMBL-EBI COVID-19 Portal (RRID:SCR_018337) Copy
DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library.
Proper citation: BOLD (RRID:SCR_004278) Copy
http://www.lcb.uu.se/lcbdw.php
A microarray-experiment oriented warehouse for collections of expression data, integrated with gene annotation profiling and used to support genomic data mining processes. It provides means to access and extract valuable information from a Laboratory Information Management System (LIMS) and makes use of several plug-ins to process and analyze the data. The system consists of two parts: MIAME compliant data storage is handled by the LIMS while data analysis is performed in the DWH. The core of the system is BASE. Accessing LIMS and DWH is accomplished through secure connections.
Proper citation: LCB-DWH (RRID:SCR_010942) Copy
http://www.einstein.yu.edu/centers/ictr/
Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research.
Proper citation: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository (RRID:SCR_005297) Copy
https://github.com/openworm/tracker-commons
Software tool as repository of documentation, software, and discussions to share worm tracking data and analysis routines.Open access repository for storing, accessing, and filtering data; interchange format for notating single or multi worm behavior; and file formats written in Python for feature extraction, review, and analysis.
Proper citation: Worm Behavior Platform (RRID:SCR_021501) Copy
http://eddylab.org/software.html
Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.
Proper citation: Eddy Lab Software (RRID:SCR_001458) Copy
https://github.com/XSLiuLab/tumor-immunogenicity-score
Repository to share analysis procedure, data and help readers or reviewers to know more detail of this work, reproduce or make use of results they are interested in.
Proper citation: TIGS (RRID:SCR_017565) Copy
Centralized, annotated repository for the Osteoarthritis Initiative (OAI) study, designed to accelerate research by organizing and linking extensive clinical, imaging (MRI/X-ray), and biomarker data. It aims to help researchers analyze knee osteoarthritis prevention, treatment, and progression.
Proper citation: OAI Knowledge base (RRID:SCR_028107) Copy
Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names.
Proper citation: NSW BioNet (RRID:SCR_019162) Copy
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