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@Arcadia-Science

Arcadia Science

README.md

Welcome to @Arcadia-Science!

At Arcadia, one of our central tenets is that our science should be maximally useful. Computational tasks are embedded in all aspects of our scientific inquiry, so we need our computing strategies to be maximally useful too. What does this mean? In addition to aligning with scientific priorities across Arcadia, we believe that useful computing is ✨ innovative, 👩‍💻usable, 🔁 reproducible.

Popular repositories Loading

  1. agentic-pymol agentic-pymol Public

    A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)

    Python 104 21

  2. glass-box-umap glass-box-umap Public

    Python package for making UMAP interpretable with exact feature contributions

    Python 54 2

  3. ProteinCartography ProteinCartography Public

    A pipeline to build similarity maps of protein space

    Jupyter Notebook 49 15

  4. readlif readlif Public archive

    Leica Image Format (LIF) file reader for Python

    Python 40 14

  5. metagenomics metagenomics Public

    A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

    Nextflow 39 5

  6. seqqc seqqc Public

    A Nextflow pipeline to identify quality control issues with new sequencing data.

    Groovy 30

Repositories

Showing 10 of 142 repositories
  • data-hub Public

    Data Hub makes lab instrument data instantly accessible to people, pipelines, and agents

    Arcadia-Science/data-hub's past year of commit activity
    TypeScript 16 MIT 3 2 1 Updated Oct 6, 2026
  • noveltree Public

    NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

    Arcadia-Science/noveltree's past year of commit activity
    Nextflow 27 AGPL-3.0 4 20 1 Updated Oct 6, 2026
  • raman-protein-analysis Public

    Python codebase for generating figures in the 2026 Arcadia Science pub titled "Spontaneous Raman spectroscopy detects chemical perturbation of protein structure".

    Arcadia-Science/raman-protein-analysis's past year of commit activity
    HTML 0 MIT 0 0 3 Updated Oct 5, 2026
  • agentic-pymol Public

    A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)

    Arcadia-Science/agentic-pymol's past year of commit activity
    Python 104 MIT 21 2 0 Updated Oct 5, 2026
  • phenotypic-geometry Public
    Arcadia-Science/phenotypic-geometry's past year of commit activity
    R 0 MIT 0 1 0 Updated Oct 5, 2026
  • notebook-pub-theme Public

    A Quarto extension that provides shared styling and infrastructure for Arcadia Science notebook publications.

    Arcadia-Science/notebook-pub-theme's past year of commit activity
    CSS 0 0 0 0 Updated Oct 1, 2026
  • 2024-auto-openraman Public

    Python package for automation and extension of OpenRaman

    Arcadia-Science/2024-auto-openraman's past year of commit activity
    Python 8 MIT 0 10 0 Updated Sep 25, 2026
  • arcadia-pycolor Public

    Python package for styling plots according to Arcadia's style guide

    Arcadia-Science/arcadia-pycolor's past year of commit activity
    Python 8 MIT 1 13 (1 issue needs help) 3 Updated Sep 24, 2026
  • beads-cell-growth Public

    Scripts and code accompanying the pub "Adding a single glass bead to liquid cultures improves cell culture quality"

    Arcadia-Science/beads-cell-growth's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 6 Updated Sep 25, 2026
  • arcadia-microscopy-tools Public

    High-throughput microscopy image analysis toolkit

    Arcadia-Science/arcadia-microscopy-tools's past year of commit activity
    Python 1 MIT 1 1 6 Updated Sep 24, 2026
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