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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.
Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.
Proper citation: ZENODO (RRID:SCR_004129) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.Digital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individuals
Proper citation: Wellcome Images (RRID:SCR_004181) Copy
An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.
Proper citation: MorphBank (RRID:SCR_003147) Copy
The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible.
Proper citation: Deciphering Developmental Disorders (RRID:SCR_006171) Copy
https://github.com/openMetadataInitiative/openMINDS_ephys
Software repository is part of the open Metadata Initiative for Neuroscience Data Structures (openMINDS). It extends openMINDS, by providing metadata schemas for in-depth descriptions of electrophysiology experiments.
Proper citation: openMINDS ephys metadata model (RRID:SCR_026250) Copy
Web based mass spectrometry ecosystem that aims to be open access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass spectrometry data. Database of mass spectrometry datasets.
Proper citation: GNPS (RRID:SCR_019012) Copy
https://github.com/blawlor/field-of-genes
Software repository holding a cloud-ready demonstration of the use of Kafka as a genomic database.
Proper citation: Field of Genes (RRID:SCR_016155) Copy
https://www.rarediseasesnetwork.org/cms/create/researchers/biorepository
Biorepository of samples collected from patients with ALS, ALS-frontotemporal dementia (ALS-FTD), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), hereditary spastic paraplegia (HSP) and multisystem proteinopathy (MSP). Used by Consortium members and the scientific community to advance therapeutic development through study of the relationship between clinical phenotype and underlying genotype, and also through the discovery and development of biomarkers.
Proper citation: CReATE (RRID:SCR_016436) Copy
http://researchdata.4tu.nl/en/home/
Multidisciplinary data repository for a consortium of universities in the Netherlands housing over datasets with a focus on scientific and technical data. Most data were produced by Dutch researchers including datasets from doctoral research. Users can deposit up to 1G by completing an upload form. Collection development foci include applied sciences, biomedical technology, earth sciences, and technology and construction. 4TU.Datacentrum is a collaboration of the libraries of the three leading technical universities - Delft University of Technology, Eindhoven University of Technology and the University of Twente.
Proper citation: 4TU.Datacentrum (RRID:SCR_006295) Copy
Tissue bank that specifically provides human tissue and cell samples for research purposes. It offers PBMCs, whole blood, solid tumor tissues, circulating tumor cells, and a variety of other bio-specimens.
Proper citation: Conversant Biologics Inc. (RRID:SCR_010675) Copy
https://knowledge.figshare.com/plus
Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability.
Proper citation: FigsharePlus (RRID:SCR_021762) Copy
http://iiif.io/#plug-’n’-play-software
Set of shared application programming interface specifications for interoperable functionality in digital image repositories. It utilizes JSON-LD, linked data, and standard W3C web protocols to parse and share digital image data, migrate across technology systems, and provide enhanced image access.
Proper citation: International Image Interoperability Framework (RRID:SCR_015029) Copy
Repository for EEG data. The International Epilepsy Electrophysiology Portal is a collaborative initiative funded by the National Institutes of Neurological Disease and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. The portal includes a large database of scientific data and tools to analyze these datasets.
Proper citation: ieeg.org (RRID:SCR_010000) Copy
https://www.umichorganoid.org/
Core enables the use of primary human organoids as tissue models for discovery, translation and regenerative medicine by providing:access to high-quality, well-characterized neonatal through adult human organoid lines from multiple organs for investigators studying human development and disease; access to detailed protocols; access to specialized, quality controlled and batch-tested reagents; expertise, guidance and training; help obtaining data;help establishing organoid lines;letters of support for grant submissions.
Proper citation: University of Michigan Human Organoid Core Facility (RRID:SCR_027333) Copy
A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.
Proper citation: Simtk.org (RRID:SCR_002680) Copy
https://github.com/scidash/neuronunit
Software toolkit for data-driven validation of neuron and ion channel models using SciUnit. NeuronUnit implements an interface to several simulators and model description languages, handles test calculations according to domain standards, and enables automated construction of tests based on data from several major public data repositories.
Proper citation: NeuronUnit (RRID:SCR_015634) Copy
Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models.
Proper citation: Scayle (RRID:SCR_019064) Copy
https://scicrunch.org/scicrunch/data/source/nlx_154697-12/search?q=*
A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.
Proper citation: Integrated Models (RRID:SCR_001481) Copy
A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler.
Proper citation: GenomeCompiler (RRID:SCR_013988) Copy
https://www.ngdc.noaa.gov/mgg/curator/
A repository of geologic material from sea floor and lakebed cores, grabs, and dredges archived by participating institutions.
Proper citation: Index to Marine and Lacustrine Geologic Samples (RRID:SCR_009430) Copy
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