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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 106 21

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

    Python package for making UMAP interpretable with exact feature contributions

    Python 55 3

  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 145 repositories
  • 2024-auto-openraman Public

    Python package for automation and extension of OpenRaman

    Arcadia-Science/2024-auto-openraman's past year of commit activity
    Python 9 MIT 0 10 4 Updated Oct 30, 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 12 Updated Oct 30, 2026
  • raman-therapeutic-discovery Public

    Code analyzing Raman spectra from tick lipids and fractions

    Arcadia-Science/raman-therapeutic-discovery's past year of commit activity
    Python 0 0 0 9 Updated Oct 30, 2026
  • cloud-scaled-cell-phenotyping Public

    Notebook pub for scaling single-cell phenotyping with Cellpose-SAM and cloud GPUs.

    Arcadia-Science/cloud-scaled-cell-phenotyping's past year of commit activity
    Jupyter Notebook 0 MIT 0 1 5 Updated Oct 30, 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 30, 2026
  • spectralora-molecular-alignment Public

    Post-training compact molecular GNNs for surrogate Raman prediction and post-hoc spectral alignment via structural prompting and derivative-free optimization via evolution strategies.

    Arcadia-Science/spectralora-molecular-alignment's past year of commit activity
    Jupyter Notebook 4 MIT 1 0 11 Updated Oct 30, 2026
  • raman-batch-effects-yeast Public
    Arcadia-Science/raman-batch-effects-yeast's past year of commit activity
    Python 0 MIT 0 0 7 Updated Oct 30, 2026
  • evo2-gene-representations Public

    Investigating gene families in the latent space of genomic language models (gLMs)

    Arcadia-Science/evo2-gene-representations's past year of commit activity
    Python 1 MIT 0 0 10 Updated Oct 30, 2026
  • glass-box-umap Public

    Python package for making UMAP interpretable with exact feature contributions

    Arcadia-Science/glass-box-umap's past year of commit activity
    Python 55 MIT 3 4 9 Updated Oct 30, 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 106 MIT 21 2 4 Updated Oct 30, 2026
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