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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.
https://mibig.secondarymetabolites.org/
MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.
Proper citation: Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) Copy
Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy
https://github.com/galaxyproteomics/mvpapplication-git.git
Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.
Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy
https://icite.od.nih.gov/covid19/search/
NIH comprehensive, curated source for publications related to COVID-19. Includes articles from PubMed and pre-prints from arXiv, medRxiv, bioRxiv, and ChemRxiv. Updated daily. NIH Office of Portfolio Analysis has developed this resource to explore and analyze set of advances in COVID‑19 research as they accumulate in real time, and complements efforts by NLM to aggregate full text documents broadly related to COVID-19 and other outbreaks, and articles on COVID‑19 specific to PubMed database.
Proper citation: NIH COVID-19 Portfolio (RRID:SCR_018295) Copy
https://datascience.nih.gov/covid-19-open-access-resources
COVID-19 open access data and computational resources provided by federal agencies, including NIH, public consortia, and private entities. Continuously updated as more information becomes available. These resources are being shared for scientific and public health interests, and content is responsibility of resource organizers.
Proper citation: Data and Computational Resources to Address COVID-19 (RRID:SCR_018274) Copy
https://ncats.nih.gov/n3c/about
Portal for centralized national data to study COVID-19 and identify potential treatments.Centralized, secure analytics platform where patient privacy is protected. Enables collection and analysis of clinical, laboratory and diagnostic data from hospitals and health care plans. Data are provided after executing data transfer agreement with National Center for Advancing Translational Sciences. N3C is partnership among NCATS supported Clinical and Translational Science Awards Program hubs and National Center for Data to Health with overall stewardship by NCATS.
Proper citation: National COVID Cohort Collaborative (RRID:SCR_018757) Copy
https://bivi.co/visualisation/apinatomy
Software toolkit for visualizing multiscale anatomy schematics with phenotype related information. Used for visualisation of multiscale physiology circuitboards and to support clinical and scientific graphical user interfaces and dashboards for biomedical resource management and data analytics. Creates FAIR models of vascular and neural connectivity information for molecular, subcellular, cellular and tissue conduits across multiple scales. Provides interface between physiology knowledge and data relevant to physiology through intuitive graphical interface for managing semantic metadata and ontologies relevant to physiology. Brings together expertise in computer science, image processing, bioengineering and medicine to manage knowledge in physiology and pathology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ApiNATOMY (RRID:SCR_018998) Copy
https://portal.imaging.datacommons.cancer.gov
Portal for finding and analyzing cancer imaging data. Part of Cancer Research Data Commons to support cancer imaging research. Provides cloud based access to medical imaging data and library of analytical tools and workflows to share, analyze, and visualize multi modal imaging data from both clinical and basic cancer research studies.
Proper citation: NCI Imaging Data Commons (RRID:SCR_019127) Copy
https://datacommons.cancer.gov
Cloud based data science infrastructure that provides secure access to cancer research data from NCI programs and key external cancer programs. Serves as coordinated resource for public data sharing of NCI funded programs. Users can explore and use analytical and visualization tools for data analysis. Enables to search and aggregate data across repositories including Cancer Data Service, Clinical Trial Data Commons, Genomic Data Commons, Imaging Data Commons, Integrated Canine Data Commons, Proteomic Data Commons.
Proper citation: Cancer Research Data Commons (RRID:SCR_019128) Copy
UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform.
Proper citation: FAIR Data Informatics Laboratory (RRID:SCR_019235) Copy
Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Agilent: Bravo NGS (RRID:SCR_019473) Copy
VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.
Proper citation: NIH VideoCasting (RRID:SCR_001885) Copy
http://tvmouse.compmed.ucdavis.edu/
Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.
Proper citation: Visible Mouse Project (RRID:SCR_002393) Copy
Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.
Proper citation: ClinicalTrials.gov (RRID:SCR_002309) Copy
A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
Proper citation: PROVEAN (RRID:SCR_002182) 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://simtk.org/home/foldvillin
An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.
Proper citation: Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) Copy
http://mialab.mrn.org/software/eegift/index.html
Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.
Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy
https://dpcpsi.nih.gov/onr/nrcc
Coordinates nutritional sciences-related research and research training across the National Institutes of Health (NIH) and among Federal Agencies by providing mechanisms to communicate research, research training, policy, and education initiatives. The DNRC facilitates the exchange of information, coordinates workshops and seminars on critical issues, encourages national and international research collaborations, and serves as the NIH primary point of contact for the Department of Health and Human Services (DHHS) and other agencies, departments, and organizations in matters pertaining to nutritional sciences and physical activity. Through its dedicated efforts to promote scientific policy reviews, innovative research, interagency collaboration, and technical advancements, the DNRC strives to define the increasing roles of nutritional sciences and physical activity in health promotion and disease prevention and treatment.
Proper citation: NIH Division of Nutrition Research Coordination (RRID:SCR_001469) Copy
http://nashua.case.edu/PathwaysWeb/Web/
An integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. The system contains a pathways database and associated tools to store, compare, query, and visualize metabolic pathways. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined and ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. The available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products.
Proper citation: PathCase Pathways Database System (RRID:SCR_001835) Copy
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