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https://github.com/openMetadataInitiative/openMINDS_stimulation
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 stimuli and stimulation protocols in neuroscience.
Proper citation: openMINDS stimulation metadata model (RRID:SCR_026253) 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
Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.
Proper citation: Arvados (RRID:SCR_002223) Copy
Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples.
Proper citation: Kidney Tissue Atlas (RRID:SCR_021626) Copy
http://arch.library.northwestern.edu/
Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.
Proper citation: Arch (RRID:SCR_023130) Copy
DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data.
Proper citation: datasets.datalad.org (RRID:SCR_019089) Copy
Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.
Proper citation: TRACK TBI Network (RRID:SCR_004723) 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
An open access repository of conference posters from across the life sciences and medicine. It provides a permanent, structured environment for the deposition of posters as well as a trustworthy venue for ongoing discussion and development of the information being presented. You can browse posters by Topic or Section or by conference. Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed. The most interesting posters are selected for evaluation by our expert Faculty and you will receive ideas and feedback. Widen your audience ����?? top performing posters receive 800+ views in a month!
Proper citation: F1000 Posters (RRID:SCR_006503) Copy
Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.
Proper citation: ProGlycProt (RRID:SCR_000622) Copy
https://github.com/openMetadataInitiative/openMINDS_specimenPrep
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 specimen preparations (surgery, tissue slicing, etc.).
Proper citation: openMINDS specimenPrep metadata model (RRID:SCR_026252) Copy
https://petab.readthedocs.io/en/latest/
Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology.
Proper citation: PEtab (RRID:SCR_026915) Copy
http://ireceptor.irmacs.sfu.ca/
Data discovery platform that facilitates curation, analysis and sharing of antibody/B-cell and T-cell receptor repertoires from multiple labs and institutions. Used to increase value of data through sharing with community. Platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.
Proper citation: iReceptor (RRID:SCR_022294) 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
A microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also. Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis.
Proper citation: M-CHiPS (RRID:SCR_010944) Copy
A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training.
Proper citation: Kitware (RRID:SCR_013989) Copy
Core is focused on supporting researchers with participant recruitment, both on a small and large scale ensuring participant recruitment reflects the population and community across Delaware and neighboring Maryland and Pennsylvania communities. CHRC coordinates research subject logistics such as screening, scheduling, transportation, and reimbursement. CHRC also provides the university community with data management education, database set-up, repository maintenance, hardening and security. CHRC supports REDCap across UD and assists researchers in building and maintaining participant registries.
Proper citation: University of Delaware Center for Human Research Coordination Core Facility (RRID:SCR_029059) Copy
Community portal for a distributed data sharing platform and open protocol for building apps. The Dat Project imagines a web of commons created by global communities on open and secure protocols.
Proper citation: Dat Project (RRID:SCR_015779) Copy
http://mona.fiehnlab.ucdavis.edu
Metadata-centric, auto-curating repository designed for storage and querying of mass spectral records. It contains metabolite mass spectra, metadata and associated compounds.
Proper citation: MassBank of North America (RRID:SCR_015536) Copy
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