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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://github.com/pmenzel/ont-assembly-snake
Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools.
Proper citation: ont-assembly-snake (RRID:SCR_024898) Copy
https://www.lsuhs.edu/centers/cardiovascular-diseases-and-sciences/cobre/cobre-core-facilities
Facility includes Analytic Redox Biology and Molecular Signaling Sub-Cores. Provided services include measurements of reactive oxygen species, reactive nitrogen species, reactive sulfide species, protein, peptides, metabolites, and lipids in cell culture and tissue samples. High-performance liquid chromatography systems, coupled with UV-vis and fluorescence detectors to quantify cellular and mitochondrial superoxide production, hydrogen sulfide pools (free sulfide, sulfide bound to transitional metals, and sulfane sulfur), and thiols (glutathione, GSH/GSSG, cysteine, cystine, homocysteine, persulfides, and glutathionylation).Instruments include Sievers NO Analyzer (NOA 280i, GE), Agilent 8890 GC and 8335 sulfur chemiluminescence detector ,Thermo Scientific Orbitrap Exploris 480 and SCIEX Triple Quad 7500 mass spectrometer. Molecular Signaling Sub-Core offers services for molecular cloning and site-directed mutagenesis, design and production of vectors for CRISPR/Cas9 modification of vascular cells, services for endothelial, smooth muscle, and cardiac myocyte cell isolation, for generation of vascular cell lines, and for lentivirus production for transient or stable modification of cardiovascular cells, access to equipment and expertise for studying cellular effects of hypoxia/reoxygenation injury (Coy Hypoxic Chamber, CLARIOstar Spectrofluorometer), for automated capillary Western blot analysis (ProteinSimple Jess Simple Western), and for high-resolution fluo-respirometry to study mitochondrial function (Oroboros O2k modular system).
Proper citation: Louisiana State University in Shreveport Redox Molecular Signaling Core Facility (RRID:SCR_024778) Copy
Core supports data analysis, network modeling, and data science research. Provides training and education opportunities.
Proper citation: Louisiana State University in Shreveport CAIPP Bioinformatics and Modeling Core Facility (RRID:SCR_024779) Copy
https://github.com/autotubularity/autotube
Software that quantifies vascular morphometry parameters like area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in vitro assays.
Proper citation: AutoTube (RRID:SCR_024815) Copy
https://github.com/PaulingLiu/scibet
Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.
Proper citation: SciBet (RRID:SCR_024743) Copy
https://snyder.ucalgary.ca/labs/live-cell-imaging/LCIoverview
Offers advanced imaging technology, as well as training and support personalized to their imaging goals and experience. Provides Technology access and training; Assisted imaging and coaching at every step of the imaging workflow, from sample preparation to data analysis; Pilot experiments and feasibility testing; Developing custom image analysis pipelines; Image analysis consultation and training; Developing and testing new instruments and devices; Full scientific and technological collaborations and partnerships; Offsite coaching, assistance and consulting ; Collaborative projects in academic, health and allied industrial sectors;
Proper citation: University of Calgary Live Cell Imaging Laboratory Core Facility (RRID:SCR_024748) Copy
https://research.manchester.ac.uk/en/equipments/mass-spectrometry-and-separations
Core is part of the University of Manchester Faculty of Science and Engineering. Facility offers support and services in chemistry, biology and materials. Mass spectrometers including Orbitraps, Ion Mobility, MALDI, DESI, hyphenated LC-MS and GC-MS apparatuses. Other instruments are HPLC systems, UHPLC systems and GC systems.
Proper citation: University of Manchester Mass Spectrometry and Separations Core Facility (RRID:SCR_024761) Copy
https://github.com/qt-creator/qt-creator?tab=readme-ov-file
Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers.
Proper citation: Qt Creator (RRID:SCR_024883) Copy
https://www.3dhistech.com/research/software-downloads/
Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research.
Proper citation: 3DHISTECH SlideViewer (RRID:SCR_024885) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC
Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components.
Proper citation: Multivariate Exploratory Linear Optimized Decomposition into Independent Components (RRID:SCR_024916) Copy
https://genomics.ccr.cancer.gov/
Core provides access to genomic technologies and Next-Generation Sequencing. Provides DNA and RNA quality control services, user accessible instrumentation, training, consultation services, bioinformatics support, and secure data delivery management.
Proper citation: NCI Center for Cancer Research Genomics Core Facility (RRID:SCR_024754) Copy
https://jmorp.megabank.tohoku.ac.jp/
Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.
Proper citation: jMORP (RRID:SCR_024755) Copy
https://www.baderc.org/cores/functional-genomics-and-bioinformatics-core/
Core provides consultative, laboratory, and bioinformatic services for next generation sequencing based applications.Core services include Pre- and post-experimental consultation to determine proper experimental approach, design, and interpretation; Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks; Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays; Library preparation, sequencing, and analysis of transcriptomes (RNA-seq), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq); Standalone sequencing on NextSeq500; Multiplexed 10x Single Cell/Nucleus Library RNA-seq Droplet generation, Library Preparation; Basic data analysis: quality assessment and normalization, genomic alignment, differential expression/enrichment, functional enrichment analysis (overrepresentation and GSEA), sample clustering, and motif enrichment; Bespoke data analysis, including integration of complex ChIP-seq and RNA-seq data sets, single-cell sequencing analyses.Core is located on the 7th floor of the Center for Life Sciences building in the Longwood Medical area (3 Blackfan Circle, CLS-728).
Proper citation: Beth Israel Deaconess Medical Center Functional Genomics and Bioinformatics Core Facility (RRID:SCR_024877) Copy
https://tnprc.tulane.edu/veterinary-medicine-research-resources
Unit is part of Tulane National Primate Research Center. Provides services including routine husbandry care for animal colonies, reporting of animals abnormal clinical signs or activities to veterinary medical staff and faculty. Animal Care Technicians provide support during diagnostic and therapeutic procedures and administration of preventive medicine program. Coordinates its activities with research personnel to provide assistance, equipment and support for their work. After hours care includes administration of treatments, collection of biologic samples for research activities and observation of animals. TNPRC facilities are accredited by Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC).
Proper citation: Tulane University TNBRC Animal Resources (RRID:SCR_024911) Copy
https://biostat.app.vumc.org/wiki/Main/PowerSampleSize
Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size.
Proper citation: PS:Power and Sample Size Calculation (RRID:SCR_024912) 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
Digital library of Internet sites and other cultural artifacts in digital form. Web history is accessible through Wayback Machine and they work with 1,200+ library and other partners through Archive-It program to identify more important web pages.
Proper citation: WaybackMachine (RRID:SCR_025022) Copy
Manually curated database of relations between phase separation and diseases.
Proper citation: PhaSeDis (RRID:SCR_024963) Copy
Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies.
Proper citation: JStor Global Plants (RRID:SCR_025018) Copy
Provides a collection of manually curated phase separation (PS) proteins and Membraneless organelles (MLOs) related proteins. Annotated phase separation-related proteins with droplet states, co-phase separation partners and other experimental information.
Proper citation: PhaSepDB (RRID:SCR_024964) Copy
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