Curator Dashboard

Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.

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• 3 years ago - submitted by Tobias Rausch

Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively.

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• 3 years ago - submitted by Kevin Chavez Lopez

Software tool for aligning and filtering, library QC, generating contact map, and identifying chromatin structures from Omni-C data.

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• 3 years ago - submitted by Gouthaman Puthan Purayil

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

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• 3 years ago - submitted by Gouthaman Puthan Purayil

Facility, located at General Campus of Ottawa Hospital, was established in 1998 and now includes three flow cytometers, two of which have sorting capabilities. Offers sorting precision required for isolation of rare cell populations with high purity and yield, up to 20 000 events per second. Allows simultaneous analysis of variety of light scatter and fluorescence parameters on single cells.

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• 3 years ago - submitted by Edyta Vieth

Flow cytometry based multiplex bead array reader with ability to simultaneously acquire data for two reporter channels per analyte. Compact, flow based, multiplex platform that combines low- and high-plex capabilities, quick time to reliable results, and ability to simultaneously acquire data for two parameters per analyte.

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• 3 years ago - by Anonymous

Lightweight, modular web-based data management platform for biomedical research projects. Introduces multiple extension modules that support scientific data management. Used for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects.

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• 3 years ago - by Anonymous

Provides infrastructure for self service sample management tools, centralized broad consent, standardized laboratory services, and long term sample storage solutions.Tracks biological samples collected in every study at Stanford and linking each with associated electronic health records (i.e., EPIC), REDCap, and molecular data.

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• 3 years ago - submitted by Edyta Vieth

Small animal imaginig service center.Instruments range from systems typically found in clinical setting, but scaled for rodent usage (such as MRI, PET, CT and ultrasound), optical systems for measuring bioluminescence, fluorescence, and Cherenkov light (IVIS, Ami, Lago and Maestro systems), new modalities (MPI and photoacoustic), as well as access to advanced image analysis software, computer workstations, and surgical preparation areas. Scientists are trained to use instruments independently and can schedule studies as needed.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Houses four whole-body MRI systems (three 3.0T, one 7.0T). 3T2 and 3T3 are part of the Lucas Service Center. Individual researchers are trained in magnet safety and scanner operations by the magnet manager or MR research technologists.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Houses whole-body PET/MRI scanner and carbon-13 hyperpolarizer device.Simultaneous PET/MRI scanner combines high spatial resolution and fine anatomical soft tissue detail of MRI with high molecular specificity of PET imaging.PMMSC is the World's first installation of a SpinLab hyperpolarizer along side a PET/MRI scanner.Individual researchers are required to undergo MR safety and radiation safety training.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Center consists of Virology BSL3 lab, separate BSL3 Bacteriology lab, and BSL2 lab. It is operated by School of Medicine as scientific service center and is open to all Stanford researchers after adequate training and subsequent use.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides broad range of tissue processing services to Stanford investigators in human disease research.Consolidates and centralizes tissue processing. Provides advice and expertise in tissue processing.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

School of Medicine service center operated by Department of Genetics.Set up to facilitate massive scale genomics at Stanford and supports omics, microbiome, sensor, and phenotypic data types.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software extensible environment for interactive and reproducible computing, based on Jupyter Notebook and Architecture. Next generation user interface for Project Jupyter offering all familiar building blocks of classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in flexible and powerful user interface. Can be extended using npm packages that use our public APIs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 3 years ago - by Anonymous

Software Python library to store NumPy arrays in TIFF (Tagged Image File Format) files, and read image and metadata from TIFF-like files used in bioimaging. Image and metadata can be read from TIFF, BigTIFF, OME-TIFF, DNG, STK, LSM, SGI, NIHImage, ImageJ, Micro-Manager NDTiff, FluoView, ScanImage, SEQ, GEL, SVS, SCN, SIS, BIF, ZIF (Zoomable Image File Format), QPTIFF (QPI, PKI), NDPI, and GeoTIFF files.

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• 3 years ago - by Anonymous

Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool.

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• 3 years ago - by Anonymous

Software provides set of wrapper functions for integration between ImageJ2 and Python. Supports original ImageJ API and data structures. Used to combine ImageJ and ImageJ2 with other tools available from Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.

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• 3 years ago - by Anonymous

Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code.

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• 3 years ago - by Anonymous

Open source project and Python package that introduces labels in form of dimensions, coordinates, and attributes on top of raw NumPy-like arrays, which allows for more intuitive, more concise, and less error-prone user experience. Includes large and growing library of domain agnostic functions for advanced analytics and visualization with these data structures.

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• 3 years ago - by Anonymous