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http://www.kegg.jp/

Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

Proper citation: KEGG (RRID:SCR_012773) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/assembly

Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).

Proper citation: NCBI Assembly Archive Viewer (RRID:SCR_012917) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://rnai.dkfz.de

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

Proper citation: GenomeRNAi (RRID:SCR_013088) Copy   

•   Source: SciCrunch Registry

https://data.mendeley.com/

Cloud-based data repository for storing, publishing and accessing scientific data. Mendeley Data creates a permanent location and issues Force 11 compliant citations for uploaded data.

Proper citation: Mendeley Data (RRID:SCR_015671) Copy   

•   Source: SciCrunch Registry

http://www.emdataresource.org/

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

Proper citation: EMDataResource.org (RRID:SCR_003207) Copy   

•   Source: SciCrunch Registry

http://sbgrid.org/

Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application.

Proper citation: Structural Biology Grid (RRID:SCR_003511) Copy   

•   Source: SciCrunch Registry

http://www.cellimagelibrary.org/

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/

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   

•   Source: SciCrunch Registry

http://www.ncats.nih.gov/research/reengineering/bridgs/bridgs.html

on a competitive basis, successful applicants receive access to NIH contractors who conduct preclinical studies at no cost to the investigator for the development of new therapeutic agents. In general, synthesis, formulation, pharmacokinetic and toxicology services in support of investigator-held Investigational New Drug (IND) applications to the Food and Drug Administration are available. Contract costs are supported by the NIH Common Fund and collaborating NIH Institutes and Centers. Access to contracts is based upon a peer-reviewed application process. The number of awards made will depend on the number of applications received, their scientific merit, and the availability of NIH funds. BrIDGs is not a complete drug development program or an unconditional commitment to develop a particular compound for the clinic. In some cases the program supports one or two key steps for preclinical development, while in other cases it assists with most of the development tasks needed to file an IND. The services provided by the program depend upon the stage of a given project and need for additional data. Once a project is approved, NIH staff work with principal investigators to develop a plan for the conduct of proposed studies. Contractors perform tasks approved by BrIDGs under the direction of NIH staff. Development proceeds sequentially in most cases and the start of one segment of the project (e.g., toxicology) may depend on satisfactory completion of preceding segments (e.g., formulation). Insurmountable difficulties in one segment may force the discontinuation of an entire project. BrIDGs supports projects proposed by academic institutions, not-for-profit organizations, and SBIR-eligible businesses. Foreign academic and non-profit institutions may also apply. Potential therapies for any disease or disorder may be submitted to BrIDGs. All proposed therapeutic agents should have demonstrated pharmacological activity in an appropriate in vivo disease model before applying.

Proper citation: Bridging Interventional Development Gaps (RRID:SCR_005635) Copy   

•   Source: SciCrunch Registry

http://www.physionet.org/

Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material.

Proper citation: PhysioNet (RRID:SCR_007345) Copy   

•   Source: SciCrunch Registry

http://www.diabetes-translation.org

Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research.

Proper citation: Centers for Diabetes Translation Research (RRID:SCR_015149) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/robucket/

Portal for open source operant chamber, based on Arduino microcontroller platform, that can be used to train mice to respond for reward. Designed by NIDDK scientists.Apparatus contains two nose pokes, drinking well, and solenoid controlled sucrose delivery system. Chamber can run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms.

Proper citation: Rodent Operant Bucket project (RRID:SCR_021565) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/geo/

Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy   

•   Source: SciCrunch Registry

http://www.proteomexchange.org

A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Proper citation: ProteomeXchange (RRID:SCR_004055) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/metabolights/

A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments.

Proper citation: MetaboLights (RRID:SCR_014663) Copy   

•   Source: SciCrunch Registry

http://cxidb.org

Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide.

Proper citation: Coherent X-Ray Imaging Data Bank (CXIDB) (RRID:SCR_014722) Copy   

•   Source: SciCrunch Registry

https://www.smir.ch/

Medical image repository to store medical research data.

Proper citation: SICAS Medical Image Repository (RRID:SCR_017420) Copy   

•   Source: SciCrunch Registry

https://anvilproject.org/

Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.

Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy   

•   Source: SciCrunch Registry

https://www.beilstein-strenda-db.org/strenda/

Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal.

Proper citation: STRENDA (RRID:SCR_017422) Copy   

•   Source: SciCrunch Registry