DOCSEARCHbyAlgolia
Submit Docs

Ganymede Platform Documentation

website·Indexed 33 days ago

https://docs.ganymede.bio/

A comprehensive platform for analyzing biological and laboratory data, featuring specialized apps for qPCR, Curve Fitting, Bioprocess monitoring, and Chromatography. The platform includes a Flow Editor for creating customizable code blocks, a Data Explorer for tabular data, and a REST API for programmatic interaction. It supports data integration via Agents and Gateways (version 5.6.44), AWS S3 bucket triggers, and Allotrope validation schemas.

Tokens
118.2K
Snippets
342
Records
973
Agent score
55%

What's inside Ganymede

  1. Overview of Ganymede Modular Analysis (MA)

    Modular Analysis (MA) allows users to develop interactive web applications from Jupyter notebooks and deploy them within their Ganymede tenant. These applications are natively integrated with Ganymede data storage, providing context-rich interfaces for data capture and analysis.

  2. Overview of the Ganymede Data Platform

    Ganymede is a cloud-based data platform designed to streamline data capture and processing between lab instruments, ELN/LIMS/analytical applications, and cloud platforms. It provides a centralized location for consolidating critical data and processing it through shared pipelines to ensure reliability and accuracy.

  3. Overview of Ganymede Self-Managed Repositories

    Self-managed repositories allow organizations to host Ganymede flow code within their own Git-based infrastructure. This provides greater control over version control, CI/CD pipelines, code governance, and ownership, allowing teams to use standard Git workflows for code reviews and branching.

  4. Overview of Ganymede File Tags

    File tags in Ganymede are used to systematically organize and categorize files (e.g., by sample ID, run purpose, or experiment step). Once applied, these tags allow users to efficiently filter and search for specific data within the file browser.

  5. Overview of the Ganymede qPCR App

    The qPCR app within the Ganymede platform is a specialized tool for analyzing quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR) data. It automates complex calculations for gene expression and viral load studies, replacing manual spreadsheet calculations with interactive visualizations and standardized workflows. Key capabilities include automated ΔΔCt calculations, multi-condition analysis, and normalization across multiple reference genes.

  6. Overview of the Bioprocess app

    The Bioprocess app is a vendor-agnostic solution for bioreactor monitoring that unifies real-time online sensor measurements and atline analytical results into a single interface. It supports all major bioreactor platforms and provides role-specific dashboards for operators (real-time deviations/alarms), scientists (detailed analytical tools), and management (high-level KPIs).

  7. Overview of the Ganymede Curve Fitting app

    The Curve Fitting app within the Ganymede platform is designed for analyzing dose-response, standard curves, and binding assays. It automates regression analysis, provides interactive outlier management, and maintains audit trails for regulatory compliance. It replaces manual spreadsheet-based curve fitting to ensure consistency across users and experiments.

  8. Overview of Ganymede Nodes

    Nodes in Ganymede provide a template structure for data extraction, processing, and API communication. They perform a base function while exposing an interface for user-defined code to allow for tailoring. In Jupyter notebooks, user-editable Nodes are identified by light blue backgrounds in SQL and Python cells. These editable cells can be committed to a repository and deployed to a workflow orchestrator using the toolbar button or the keyboard shortcut Cmd+Shift+S (macOS) / Ctrl+Shift+S (Windows/Linux).

  9. Overview of the Chromatography app

    The Chromatography app is a vendor-agnostic solution designed for analytical and biopharma laboratories to collect, process, and interpret chromatographic data. It supports instruments including HPLC, UHPLC, GC, and capillary electrophoresis systems (CE-SDS). The app provides real-time visualization, intelligent peak detection, and quality control tracking with full audit trails for compliance.

  10. Overview of Ganymede Virtualization

    Virtualization is an add-on platform feature that allows users to integrate manual, locally executed analyses (such as flow cytometry gating, protein structure analysis, or microscopy image analysis) into data processing workflows. It provides a scalable environment for interactive analysis while ensuring traceability of users, input/output files, and access history. It also supports the use of encrypted files or proprietary binaries within a structured data pipeline.

  11. Read Instron Tensile .is_tens files into Ganymede data lake

    The Instron Tensile Read node reads the contents of .is_tens files and passes them to a user-defined Python function. This function processes the files and returns one or more tables to be stored in the Ganymede data lake. The node manages three primary output tables: one for file associations, one for raw metadata, and one for material dimensions.

  12. Meet Ganymede Agent hardware and OS requirements

    To ensure the Agent can communicate with Ganymede Cloud, the host machine must meet the following specifications:

    Hardware:

    • Processor: Intel i3 or newer (x86/x64 architecture)
    • RAM: Minimum 4GB (more recommended for heavy workloads)
    • Disk Space: Minimum 10GB free

    Operating System:

    • Windows 10 or newer (with display)
    • Ubuntu/Debian Linux (prior to End of Life)
    • OS must be up to date with the latest patches and updates

    Permissions:

    • Administrative access is required during installation to allow the Agent to run as a service and launch automatically on system startup.