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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.
Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.
Proper citation: X2K Web (RRID:SCR_023624) Copy
http://www.wormguides.org/home
A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase.
Proper citation: WormGUIDES (RRID:SCR_013733) Copy
Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.
Proper citation: EchinoBase (RRID:SCR_013732) Copy
Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.
Proper citation: Zebrafish International Resource Center (RRID:SCR_005065) Copy
http://medicine.tamhsc.edu/irm/msc-distribution.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Center for cell line distribution and stock at Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine. Scott & White have received a grant funded by the NIH to provide well-characterized human adult stem cells, rat stem cells, and mouse stem cells to academic researchers worldwide upon request.
Proper citation: Texas A and M Health Science Center MSC Distribution (RRID:SCR_005522) Copy
Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.
Proper citation: California National Primate Research Center (RRID:SCR_006426) 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
https://www.aplysia.earth.miami.edu/
Center where Aplysia californica are cultured and raised for research purposes. Aplysia from the facility serve in research on genomics, human brain function, toxicology for developmental studies, natural products, chemistry for isolation of novel anti-tumor and antibacterial compounds, in the study of transport by digestive tissues and have potential for use in studies of substance addiction and nerve senescence and regeneration.
Proper citation: National Resource for Aplysia (RRID:SCR_008361) Copy
https://maayanlab.cloud/sigcom-lincs
Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.
Proper citation: SigCom LINCS (RRID:SCR_022275) Copy
https://yanglab.nankai.edu.cn/trRosetta/
Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets.
Proper citation: trRosetta (RRID:SCR_021181) Copy
https://appyters.maayanlab.cloud
Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms.
Proper citation: Appyters (RRID:SCR_021245) Copy
SMBRR maintains the only self-sustaining national research resource of laboratory-born squirrel monkeys, their tissues and other biological materials, as well as the expertise to carry out research on this animal. Scientists with NIH grants utilize squirrel monkeys to study many diseases that threaten human health including Alzheimer's disease and other disorders of the central nervous system, drug addiction, malaria, and viral diseases. Center that carries out research on squirrel monkey biology and its research uses. It meets the needs of the biomedical research community in three ways: providing national resource for laboratory-born squirrel monkeys, having active research component that continues to add new information about the biology of the squirrel monkey with a particular emphasis on reproduction and colony management, and acts as a source of expertise for squirrel monkey biology, management and husbandry.
Proper citation: Squirrel Monkey Breeding and Research Resource (RRID:SCR_006291) Copy
https://maayanlab.cloud/drugmonizome/#/
Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis.
Proper citation: Drugmonizome (RRID:SCR_024821) Copy
Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.
Proper citation: Daphnia Atlas (RRID:SCR_024913) Copy
https://research.med.psu.edu/core-facilities/atomic-force-microscopy-core/
Provides College of Medicine research community with access to atomic force microscopy equipment and expertise.
Proper citation: Penn State Hershey College of Medicine Atomic Force Microscopy Core Facility (RRID:SCR_025075) Copy
https://github.com/sokrypton/ColabFold
Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.
Proper citation: ColabFold (RRID:SCR_025453) Copy
https://www.unmc.edu/vcr/cores/vcr-cores/confocal-microscopy/index.html
Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.
Proper citation: University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) Copy
https://www.utsouthwestern.edu/labs/qlmc/
Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros.
Proper citation: University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility (RRID:SCR_022605) Copy
https://www.lji.org/research/research-services/sequencing/
Core provides latest sequencing technology combined with Institute's expansive bioinformatics capabilities. Provides instrumentation including Illumina Miseq, Covaris Model E220, NovaSeq 6000, Agilent 2200 Tapestation, Beckman Coulter Biomek FXP, HiSeq 2500.
Proper citation: La Jolla Institute for Immunology Next Generation Sequencing Core Facility (RRID:SCR_023107) Copy
Multidisciplinary data generation project which aims to create and share multimodal dataset optimized for artificial intelligence research in type 2 diabetes. At each release of the AI-READI dataset, two sets will be made available: public access and controlled access set. The public set will be stripped of Protected Health Information (PHI) as well as information related to the sex and race/ethnicity of the participants.
Proper citation: AI-READI (RRID:SCR_027031) Copy
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