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https://swmath.org/

Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software.

Proper citation: swMath (RRID:SCR_017607) Copy   

•   Source: SciCrunch Registry
  

http://www.technicalreports.org/trail/search/

Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT.

Proper citation: Trail Technical Report Archive (RRID:SCR_017324) Copy   

•   Source: SciCrunch Registry
  

http://www.conceptwiki.org

A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki.

Proper citation: ConceptWiki (RRID:SCR_006362) Copy   

•   Source: SciCrunch Registry
  

http://sumsdb.wustl.edu/sums/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

Proper citation: SumsDB (RRID:SCR_002759) Copy   

•   Source: SciCrunch Registry
  

https://github.com/openMetadataInitiative/openMINDS

The openMINDS metadata framework comprises: schema specifications for multiple, interlocked metadata models for Linked Data, instance libraries for serviceable, well defined terms and constructs, as well as supportive tooling. openMINDS is developed as open source project by Open Metadata Initiative on GitHub. The framework is distributed over multiple, interlinked GitHub projects with one main GitHub repository for central access and maintenance.

Proper citation: openMINDS metadata framework (RRID:SCR_023173) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/genouest/biomaj

Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.

Proper citation: BioMAJ (RRID:SCR_023983) Copy   

•   Source: SciCrunch Registry
  

http://caintegrator-info.nci.nih.gov/rembrandt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory.

Proper citation: Glioma Molecular Dignostic Initiatives (RRID:SCR_003329) Copy   

•   Source: SciCrunch Registry
  

http://genome.ucsc.edu/ENCODE

Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.

Proper citation: ENCODE (RRID:SCR_006793) Copy   

•   Source: SciCrunch Registry
  

https://www.dataone.org/

A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community.

Proper citation: DataONE (RRID:SCR_003999) Copy   

•   Source: SciCrunch Registry
  

https://fairdomhub.org/

Initiative to develop community, and establish internationally sustained data and model management service to European Systems Biology community. Web accessible repository for storing and sharing data, models, protocols and publications relating to systems biology research projects.Repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) data, operating procedures and models.Contains data, SOPs models, publications and other research assets from large research programmes and independent projects, including SysMO consortium, ERASyAPP and Digital Salmon. Public service for users to upload and publish research assets.

Proper citation: FAIRDOMHub (RRID:SCR_021119) Copy   

•   Source: SciCrunch Registry
  

http://zebrafishucl.org/zebrafishbrain#about-1

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

Proper citation: Zebrafish Brain Atlas (RRID:SCR_000606) Copy   

•   Source: SciCrunch Registry
  

http://flowrepository.org

A database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt data standard.

Proper citation: FLOWRepository (RRID:SCR_013779) Copy   

•   Source: SciCrunch Registry
  

http://dash.harvard.edu/

Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.

Proper citation: Digital Access to Scholarship at Harvard (RRID:SCR_004122) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/genbank/dbest/

Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms.

Proper citation: dbEST (RRID:SCR_008132) Copy   

•   Source: SciCrunch Registry
  

https://fitbir.nih.gov/

Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.

Proper citation: Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) Copy   

•   Source: SciCrunch Registry
  

http://PlasmoDB.org

Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.

Proper citation: PlasmoDB (RRID:SCR_013331) Copy   

•   Source: SciCrunch Registry
  

http://vectormap.si.edu/

Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.

Proper citation: VectorMap (RRID:SCR_016721) Copy   

•   Source: SciCrunch Registry
  

https://tbportals.niaid.nih.gov

Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.

Proper citation: TB PORTALS (RRID:SCR_016594) Copy   

•   Source: SciCrunch Registry
  

https://t1dexchange.org/research/biobank/

Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.

Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy   

•   Source: SciCrunch Registry