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HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Main workflow is Literature Review. If you ask question, Elicit will show relevant papers and summaries of key information about those papers in easy-to-use table.
Proper citation: Elicit (RRID:SCR_023362) Copy
Productivity and collaboration PDF solution, combining Acrobat desktop software, mobile scan app, signature app and Acrobat Reader mobile app enhanced with premium mobile features and premium Document Cloud services.
Proper citation: Adobe Acrobat Pro (RRID:SCR_023361) Copy
https://github.com/openMetadataInitiative/openMINDS_SANDS
One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions.
Proper citation: openMINDS SANDS metadata model (RRID:SCR_023498) Copy
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
Proper citation: Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) Copy
http://github.com/VH-Lab/vhlab-TwoPhoton-matlab
Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab.
Proper citation: vhlab-TwoPhoton-matlab (RRID:SCR_023369) Copy
https://bdcw.org/MetGENE/index.php
Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype.
Proper citation: MetGENE (RRID:SCR_023402) Copy
https://github.com/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
Eppendorf manual, autoclavable, air-cushion pipette for accurate ergonomic pipetting of aqueous solutions.
Proper citation: Eppendorf: Research plus 100-1000 uL 1 channel pipette (RRID:SCR_023466) Copy
Mechanical and autoclavable, manual, air cushion pipette for accurate, ergonomic pipetting of aqueous solutions.
Proper citation: Eppendorf: Research plus 2 ��� 20 ��L yellow 1 channel pipette (RRID:SCR_023465) Copy
Mechanical and autoclavable, manual, air cushion pipette for accurate, ergonomic pipetting of aqueous solutions.
Proper citation: Eppendorf: Research plus 20 ��� 200 ��L yellow 1 channel pipette (RRID:SCR_023464) Copy
Chromatography system for purification in research applications. Allows for customization due to its modular design with flow rate. Available with flow rate of up to 25 mL/min or flow rate of up to 150 mL/min. Offers more than 20 hardware options for custom system, including new UV monitor.Includes Air sensor L9;CELL 2 U KPL;Conductivity monitor C9n Cpl;Injection valve V9-Inj;Instrument control unit, I9, Äkta pure; Mixer M9;Pressure monitor R9-2 with pump restrictor; Pump P9 Cpl 2x; UV Monitor U9-L Cpl;Fraction collector F9-R, Cytiva, CAT# 29011362;Superdex 200 increase 10/300 GL, Cytiva, CAT# 28-9909-44.
Proper citation: Cytiva: AKTA pure 25 L chromatography system (RRID:SCR_023461) Copy
https://www.vilber.com/company/
Life science company that develops and manufacture imaging and analyzing systems for fluorescence, chemiluminescence and bioluminescence applications.
Proper citation: Vilber (RRID:SCR_023580) Copy
http://jupyterlab.github.io/jupyterlab/
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.
Proper citation: JupyterLab (RRID:SCR_023339) Copy
https://www.nanoentek.com/theme/nanont2_en/shop/02/product01_view.php?it_id=1547538993
Bench top size cell counter that is designed to count cells and verify viability accurately and precisely, using standard trypan blue technique and provides image analysis for cell counting.
Proper citation: NanoEntek: EVE Automated Cell Counter (RRID:SCR_023459) Copy
https://pillow.readthedocs.io/en/stable/
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.
Proper citation: pillow (RRID:SCR_023337) Copy
https://github.com/imagej/pyimagej
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.
Proper citation: PyImageJ (RRID:SCR_023336) Copy
https://lifesciences.tecan.com/microplate-washers-hydrospeed?p=tab--1
Advanced plate washer, designed for quick, parallel washing of entire 96- and 384-well plates. This avoids time differences between wells for uniform results. Provides full control of wash power for optimized washing of cells, beads and ELISAs. Equipped with 96 and 384 indexing wash head and optimized magnetic carriers.
Proper citation: Tecan: HydroSpeed plate washer (RRID:SCR_023457) Copy
https://github.com/tobiasrausch/alfred
Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.
Proper citation: Alfred (RRID:SCR_023354) Copy
https://github.com/neurobio-hiroshima/WRAQ
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.
Proper citation: Wheel Running Activity acQuisition (RRID:SCR_023353) Copy
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