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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Used to store, publish and share research data in FAIR way. Facilitates research data storage, guarantees long-term persistence of data and allows data, results or ideas to be shared worldwide.Supports community domains with metadata extensions, access rules and publishing workflows.
Proper citation: B2SHARE Eudat (RRID:SCR_023135) Copy
http://senselab.med.yale.edu/cellpropdb
A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid
Proper citation: Cell Properties Database (RRID:SCR_007285) Copy
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Proper citation: Synapse (RRID:SCR_006307) Copy
Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators.
Proper citation: mAdb (RRID:SCR_006677) Copy
http://brainandsociety.org/the-brain-observatory
Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.
Proper citation: Brain Observatory (RRID:SCR_010641) Copy
The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world.
Proper citation: Culture Collection of Algae at the University of Texas (RRID:SCR_016782) Copy
https://uhnbiospecimenservices.com/
Core provide services for the enhancement and progression of novel and innovative research and discovery. Provides human biospecimen samples such as: fresh frozen and formalin fixed paraffin embedded (FFPE) tissue, compartmentalized blood components such as serum, plasma, and whole blood peripheral blood mononuclear cells (PBMCs) and other biofluids, including saliva and urine; Tissue microarray (TMA) construction and quantitative image analysis of TMA sections, Laser capture microdissection (LCM), digital slide scanning, quantitative image, and pathological/clinical analysis for various tumour sites and DNA/RNA extraction; support and guidance to researchers and biobanks on accessing, collecting, and using human biospecimens and associated data for health research.
Proper citation: University Health Network Biospecimen Services Core Facility (RRID:SCR_027519) Copy
http://publications.aston.ac.uk/
Aston Publications Explorer is Aston University's repository for their open access publications. You may also be interested in Aston Data Explorer for Aston's research data and Aston Research Explorer for broader information about Aston's research work including research staff, awards and activities projects and research groups.
Proper citation: Aston Publications Explorer (RRID:SCR_023129) Copy
Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.
Proper citation: MaizeGDB (RRID:SCR_006600) Copy
Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution.
Proper citation: Fruit Fly Brain Observatory (RRID:SCR_019244) Copy
http://oncowiki.info/index.php?title=Main_Page
A free repository for oncology information, chemotherapy protocols, and cancer treatment regimens. It is meant for Healthcare providers working in the field of Oncology.
Proper citation: Onco Wiki (RRID:SCR_005002) Copy
https://nsidc.org/data/programs/eloka
Project portal to collect, preserve, and exchange local observations and Indigenous Knowledge. Collaborates with Arctic communities and Indigenous organizations, schools, and researchers to create customized data management products. ELOKA provides open and tailored data access, data stewardship for Indigenous communities, and services ranging from advising on data sharing ethics and protocols to handling different data types. Interactive digital atlases showcasing community-based observations of social and environmental change and related geospatial data, such as trail locations, place names, land-use demarcations, or local climate information. Customized websites containing cultural, historical, and/or environmental information significant to partner communities, often in the form of written interview transcripts, audio or video files, photographs, artwork, illustrations, and maps. Data sets of environmental and wildlife observations collected by Indigenous experts. Access to local weather station data, including temperature, snow thickness, and wind data.
Proper citation: ELOKA (RRID:SCR_026990) Copy
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay&cmd=search
Data and information collection and repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). Used to select and summarize the bioactivities of tested substances.
Proper citation: PubChem BioAssay (RRID:SCR_010734) Copy
Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community.
Proper citation: Astrobiology Habitable Environments Database (RRID:SCR_023133) Copy
http://neuroinformatics.kiv.zcu.cz/articles/read/eegerp-portal-eegbase-_2014-12-19
EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework.
Proper citation: EEGbase (RRID:SCR_001452) Copy
Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.
Proper citation: Open Science Framework (RRID:SCR_003238) Copy
https://phenome.jax.org/centers/QTLA
Raw data from various QTL (quantitative trait loci) studies using rodent inbred line crosses. Data are available in the .csv format used by R/qtl and pseudomarker programs. In some cases analysis scripts and/or results are posted to accompany the data. These data are provided as a courtesy to the genetic mapping community and may be used for purposes of developing or testing new analysis methods or software and for meta-analysis of quantitative traits. The authors of the datasets retain individual ownership of the data. As a courtesy to the authors, please alert them in advance of any publications that result from reanalysis of these data or obtain permission prior to redistribution of data or results. In all data sets and files, the marker locations have been translated to Cox build 37 coordinates unless otherwise stated. Please consider contributing your data to the QTL Archive.
Proper citation: QTL Archive (RRID:SCR_006213) Copy
http://www.gigasciencejournal.com/
An online open-access open-data journal, publishing ''big-data'' studies from the entire spectrum of life and biomedical sciences whose publication format links standard manuscript publication with its affiliated database, GigaDB, that hosts all associated data, provides data analysis tools, cloud-computing resources, and a DOI assignment to every dataset. GigaScience covers not just ''omic'' type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale sharable data. Supporting the open-data movement, they require that all supporting data and source code be publicly available in a suitable public repository and/or under a public domain CC0 license in the BGI GigaScience database. Using the BGI cloud as a test environment, they also consider open-source software tools / methods for the analysis or handling of large-scale data. When submitting a manuscript, please contact them if you have datasets or cloud applications you would like them to host. To maximize data usability submitters are encouraged to follow best practice for metadata reporting and are given the opportunity to submit in ISA-Tab format.
Proper citation: GigaScience (RRID:SCR_006565) Copy
Database for MHC antigenic peptide of Mycobacterium tuberculosis. It aims to make a comprehensive repository of synthetic antigenic peptides predicted from several MHC predication servers.
Proper citation: PeMtb (RRID:SCR_016278) Copy
Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome.
Proper citation: SoyBase (RRID:SCR_005096) Copy
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