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https://astrocyte.rnaseq.sofroniewlab.neurobio.ucla.edu
Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions.
Proper citation: Astrocyte Reactivity RNA-Seq Browser (RRID:SCR_015033) Copy
Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses.
Proper citation: Nonhuman Primate Reagent Resource (RRID:SCR_012986) Copy
The NCBCs are a set of networked computation core facilities for biomedical infrastructure funded under the NIH Common Fund, the National Program of Excellence in Biomedical Computing (NPEBC). There are seven funded Centers that cover systems biology, image processing, biophysical modeling, biomedical ontologies, information integration, and tools for gene-phenotype and disease analysis. The centers will create innovative software programs and other tools that enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease. Each Center has Cores that are focused on (1) computational science, (2) biomedical computational science and (3) driving biological projects whose intent is to drive the interaction between computational and biomedical computational science. In addition to the Centers, the NIH has a number of active program announcements to develop collaborations with the biomedical research community��this includes announcements from the Biomedical Information Science and Technology Initiative (BISTI) and the Program for Collaborations with National Centers for Biomedical Computing. There are numerous efforts in education and training that emanate from the Centers and there is an annual all hands meeting.
Proper citation: National Centers for Biomedical Computing (RRID:SCR_010635) Copy
https://www.ebi.ac.uk/intact/complex/#annotations:fIzBXhJPEeej78Pl6R0ScA
Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download.
Proper citation: Complex Portal (RRID:SCR_015038) Copy
Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.
Proper citation: Inxight (RRID:SCR_016490) Copy
https://www.niaid.nih.gov/about/cyber-infrastructure-computational-biology-contacts
Office of Cyber Infrastructure and Computational Biology of NIAID.
Proper citation: OCICB (RRID:SCR_016597) Copy
https://www.jax.org/news-and-insights/2013/february/komp2-mice-phenotyping-and-availability
Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River ).
Proper citation: KOMP2 (RRID:SCR_017528) Copy
https://scienceofbehaviorchange.org/about/
Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach.
Proper citation: Science of Behavior Change Research Network (RRID:SCR_017385) Copy
https://github.com/marbl/MashMap
Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.
Proper citation: MashMap (RRID:SCR_022194) Copy
https://mass-spec.stanford.edu/instruments
System includes Thermo Orbitrap Eclipse Tribid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Proper citation: Thermo Orbitrap Eclipse nanoLC/MS system (RRID:SCR_022212) Copy
https://kidsfirstdrc.org/portal/portal-features/
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Proper citation: BeWith (RRID:SCR_016573) Copy
https://www.synapse.org/#!Synapse:syn22345748/wiki/605339
Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.
Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy
https://nwb-extensions.github.io/
Community led catalog of extensions to Neurodata Without Borders data standard.
Proper citation: Neurodata Extensions Catalog (RRID:SCR_021340) Copy
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
http://grantome.com/grant/NIH/U01-DK099919-04S1
Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium.
Proper citation: Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) Copy
https://bioinfo3d.cs.tau.ac.il/PatchDock/
Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles.
Proper citation: PatchDock (RRID:SCR_017589) Copy
Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.
Proper citation: immuneXpresso (RRID:SCR_017578) Copy
https://commonfund.nih.gov/hubmap
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy
https://blake.bcm.edu/emanwiki/EMAN2
Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.
Proper citation: EMAN (RRID:SCR_016867) Copy
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