Tools   Select Another Resource Report Type

https://github.com/BioDepot/nbdocker

Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.

Proper citation: nbdocker (RRID:SCR_017159) Copy   

•   Source: SciCrunch Registry

https://github.com/DReichLab/AdmixTools

Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy   

•   Source: SciCrunch Registry

https://github.com/bondarevts/flucalc

Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis.

Proper citation: FluCalc (RRID:SCR_019322) Copy   

•   Source: SciCrunch Registry

https://github.com/sqjin/CellChat

Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.

Proper citation: CellChat (RRID:SCR_021946) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry

https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

http://snyderome.stanford.edu/

Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.

Proper citation: iPOP (RRID:SCR_008991) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/

Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications.

Proper citation: Center for Computational Mass Spectrometry (RRID:SCR_008161) Copy   

•   Source: SciCrunch Registry

http://msr.dom.wustl.edu/

Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry

Proper citation: NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) Copy   

•   Source: SciCrunch Registry

http://glycotech.ccrc.uga.edu/

Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects.

Proper citation: Resource for Integrated Glycotechnology (RRID:SCR_009008) Copy   

•   Source: SciCrunch Registry

https://bioams.llnl.gov/

Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers.

Proper citation: National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) Copy   

•   Source: SciCrunch Registry

http://cell.ccrc.uga.edu/world/glycomics/glycomics.php

Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses.

Proper citation: Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) Copy   

•   Source: SciCrunch Registry

http://www-ssrl.slac.stanford.edu/content/science/ssrl-smb-program

Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis.

Proper citation: SSRL Structural Molecular Biology (RRID:SCR_009000) Copy   

•   Source: SciCrunch Registry

https://web.uri.edu/riinbre/mic/

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

Proper citation: Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) Copy   

•   Source: SciCrunch Registry

https://core.bioinformatics.udel.edu

CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.

Proper citation: University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) Copy   

•   Source: SciCrunch Registry

https://med.und.edu/imaging/index.html

Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school.

Proper citation: University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) Copy   

•   Source: SciCrunch Registry

http://www.uwyo.edu/microscopy/

Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment.

Proper citation: Wyoming University Jenkins Microscopy Core Facility (RRID:SCR_017758) Copy   

•   Source: SciCrunch Registry

https://www.unr.edu/proteomics

Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling.

Proper citation: University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) Copy   

•   Source: SciCrunch Registry

http://psf.cobre.ku.edu/cores/ppg/about

Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies.

Proper citation: Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) Copy   

•   Source: SciCrunch Registry

http://bioimaging.dbi.udel.edu

Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies.

Proper citation: University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) Copy   

•   Source: SciCrunch Registry