Projects

Innovative open-source projects designed to empower cutting-edge bioinformatics and molecular biology

Multi-omics Analysis Infrastructure, Pipelines, and Data Management

  • daylily: cost calculator & whitepaper ( ~ $3 to $4 per 30x noamp WGS fastq->VCF )
    • Industry-leading accuracy, speed, cost, auditability, scalability, QC views & observability.
    • Reproducible, sustainable, growing & open-source omics analysis workflows. Compatible with all workflow orchestration frameworks.
    • Automated infrastructure management with comprehensive predictive and real-time cost visibility: storage / data transfer / compute.
    • Open source and free: Bloom can be deployed in 30min & fastq->VCF analysis can complete w/in 60-90min.
  • snakemake-executor-plugin-pcluster-slurm: A Snakemake executor plugin designed to interface with AWS ParallelClusters implementation of the Slurm workload manager.

Laboratory Information Management Systems (LIMS)

  • bloom: A templated, abstract, polymorphic, and opinionated LIMS designed for efficient laboratory data management.
  • zebra_day: A Zebra Label Printing library and API for network-connected printers, allowing centralized management of zebra printers throughout the lab.

API Wrappers and Integrations

  • xcures_day: This Python wrapper for the Xcures REST API facilitates seamless integration with Xcures services.
  • fedex_tracking_day: A Python module interfacing with the FedEx Tracking API, enabling programmatic tracking of shipments.

Image Processing Tools

  • img_stitcher_day: A tool for merging images of a tube's exterior, enabling comprehensive image analysis.

Color Space Conversion Utilities

  • rgbw_colorspace_converter: A utility for RGB to RGBW translation/conversion, also operating with HSV, HSI, HSL, and HEX color spaces, with a focus on LED-based projects.

Obsidian Integration Tools

  • gravity_well: A tool to import text, markdown, and PDF files into Obsidian as new notes, adding NLP-derived tags and tracking other properties.

Artistic Projects

  • pyramidtriangles: A utility for RGB to RGBW conversion, supporting HSV, HSI, HSL, and HEX color spaces, designed for LED-based projects.