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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.
http://www.biomedicumgenomics.fi/
Organization that provides academic and industrial clients access to functional genomics technologies, services and partnering solutions including genome-wide expression, copy number profiling, miRNA expression, DNA-protein interaction (ChIP-on-chip), Illumina high-throughput sequencing including nucleic acid quality and quantity assessment. For gene silencing and ectopic expression purposes, they offer high-titer shRNA and ORF lentiviruses targeting genes of interest. They also offer customized services e.g. preparation of gain or loss-of-function cell lines and protein interactomics-based services (yeast two-hybrid). In addition, they provide access to wide array of computational data analyses. BMGen also offers partnering deals for clients interested in customized integration of several technologies.
Proper citation: Biomedicum Genomics (RRID:SCR_003907) Copy
A Swiss service and consulting company specialized in the computational analysis of biomarker data from clinical trials. Their technical expertise spans across multiple biomaker technological platforms such as genetics, transcriptomics, protein assays and cellular assays. Quartz Bio is a spin-off of Merck Serono with the capital of the company entirely owned by its employees.
Proper citation: Quartz Bio (RRID:SCR_003919) Copy
http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html
Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
Proper citation: EDASeq (RRID:SCR_006751) Copy
Bioanalyzer system is automated electrophoresis tool that providesa analytical evaluation of various samples types in many workflows, including next generation sequencing NGS, gene expression, biopharmaceutical, and gene editing research. Digital data is provided in timely manner and delivers assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for accurate result, and data may be exported in many different formats.
Proper citation: Agilent 2100 Bioanalyzer Instrument (RRID:SCR_018043) Copy
http://www.sigmaplot.com/products/sigmaplot/
Statistical analysis and scientific graphing software for Windows OS.
Proper citation: SigmaPlot (RRID:SCR_003210) Copy
http://metap.helmholtz-muenchen.de/metap2/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments.
Proper citation: MetaP (RRID:SCR_014686) Copy
XSEDE is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services things like supercomputers, collections of data and new tools to improve our planet. XSEDE resources may be broadly categorized as follows: High Performance Computing, High Throughput Computing, Visualization, Storage, and Data Services. Many resources provide overlapping functionality across categories. Scientists, engineers, social scientists, and humanists around the world - many of them at colleges and universities - use advanced digital resources and services every day. Things like supercomputers, collections of data, and new tools are critical to the success of those researchers, who use them to make our lives healthier, safer, and better. XSEDE integrates these resources and services, makes them easier to use, and helps more people use them. XSEDE supports 16 supercomputers and high-end visualization and data analysis resources across the country. Digital services, meanwhile, provide users with seamless integration to NSF''s high-performance computing and data resources. XSEDE''s integrated, comprehensive suite of advanced digital services will federate with other high-end facilities and with campus-based resources, serving as the foundation for a national cyberinfrastructure ecosystem. Common authentication and trust mechanisms, global namespace and filesystems, remote job submission and monitoring, and file transfer services are examples of XSEDE''s advanced digital services. XSEDE''s standards-based architecture allows open development for future digital services and enhancements. XSEDE also provides the expertise to ensure that researchers can make the most of the supercomputers and tools.
Proper citation: XSEDE - Extreme Science and Engineering Discovery Environment (RRID:SCR_006091) Copy
Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download.
Proper citation: CaspBase (RRID:SCR_018975) Copy
Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.
Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy
A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.
Proper citation: Wakari (RRID:SCR_013995) Copy
http://cran.r-project.org/web/packages/muma/
Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).
Proper citation: MUMA (RRID:SCR_002412) Copy
https://cdtr.wustl.edu/our-cores/health-informatics/
Core facility whose services include consultation for management of complex datasets and literature resources, as well as promoting education of data analysis tools for researchers.
Proper citation: Washington University Center for Diabetes Translation Research Health Informatics in Diabetes Research Core (RRID:SCR_015206) Copy
https://www.ualberta.ca/medicine/research/corefacilities/flow-cytometry-facility/index.html
Flow Cytometry Facility offers analytical flow cytometry, cell sorting and data analysis.Instruments include FACSArias, FACSCanto II, LSR-Fortessas, Attune NxT, and Amnis ImageStream mkII.
Proper citation: University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility (RRID:SCR_019195) Copy
https://www.uclalipidomics.net/
Offers automated sample preparation and two distinct mass spectrometry platforms with services, ranging from shotgun lipidomics to isotope labeling and mathematical modeling of lipid flux parameters.Offers data analysis and consultation services to provide users with accurate analysis of lipid metabolic parameters.
Proper citation: University of California at Los Angeles Lipidomics Lab Core Facility (RRID:SCR_019210) Copy
https://ibsc.ucsc.edu/facilities/cell-culture-facility
Provides services for culture and analysis of stem cells. Provides space for embryonic stem cell growth and manipulation. Facility staff offers expertise in experimental design, protocol development, and data analysis.Equipment including biosafety hoods, centrifuges, microscopes.
Proper citation: University of California at Santa Cruz Institute for Biology of Stem Cells Cell Culture Core Facility (RRID:SCR_021353) Copy
https://www.age.mpg.de/science/core-facilities/facs-imaging
Provides equipment including wide field and confocal microscopes, flow cytometry analyzers and sorters, shared histology equipment, and PC workstations for data analysis.Provides services such as software training, access to analysis software, and help with experimental planning and post acquisition analysis.
Proper citation: Max Planck Institute for Biology of Ageing FACS and Imaging Core Facility (RRID:SCR_021354) Copy
https://nybloodcenter.org/lindsley-f-kimball-research-institute/core-facilities/flow-cytometry/
Core provides in house investigators and external clients with equipment for multiparameter flow cytometric analysis and cell sorting, training and expert assistance with various techniques in flow cytometry,cell sorting as well as consultation in experimental design, data analysis, presentation, and publication.
Proper citation: LFKRI New York Blood Center Flow Cytometry Core Facility (RRID:SCR_021779) Copy
https://www.cincinnatichildrens.org/research/cores/dna-sequencing-genotyping
Supports production and analysis of DNA and RNA related data. Provides DNA and RNA sequencing, Next Generation sequencing, DNA extraction and high and low throughput SNP genotyping.
Proper citation: Cincinnati Children's Hospital DNA Sequencing and Genotyping Core Facility (RRID:SCR_022630) Copy
https://www.fredhutch.org/en/research/shared-resources/core-facilities/proteomics-metabolomics.html
Provides support for mass spectrometry based proteomics and metabolomics research. With advanced instrumentation and highly trained staff, core offers consultation and services in sample preparation, sample separation, data collection and data analysis.
Proper citation: Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility (RRID:SCR_022618) Copy
https://voices.uchicago.edu/metabolomics/
Equipped with Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer(+UVPD)- Vanquish Horizon UHPLC system. Provides experience in quantifying diverse groups of metabolites in cells, culture medium, bodily fluid, animal tissue, exhaled breath condensate, etc., and performes stable isotope tracing experiments using 13C, 15N, and 2H-labeled substrates. Support hypothesis generating untargeted and hypothesis driven targeted metabolomics studies from experimental design stage through data acquisition, data analysis, and interpretation.
Proper citation: University of Chicago Metabolomics Platform Core Facility (RRID:SCR_022932) Copy
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