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    136 repositories

    • ramanalysis

      Public
      Package for loading and processing spectral data from Arcadia's Raman spectroscopy instruments.
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 14, 2026Jul 14, 2026

    • arcadia-pycolor

      Public
      Python package for styling plots according to Arcadia's style guide
      plotlymatplotlib
      plotlymatplotlib
      Python
      •
      MIT License
      •1•7•13•1•Updated Jul 13, 2026Jul 13, 2026

    • 2024-disco-raman-hackathon

      Public
      This repo is intended to hold code and results pertaining to the raman hackathon carried out by the discovery team at the discovery offsite in March 2024.
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jul 6, 2026Jul 6, 2026

    • 2024-predicting-antimicrobial-resistance

      Public
      Analyses of large scale E. coli metagenome diversity data
      R
      •0•1•0•1•Updated Jul 6, 2026Jul 6, 2026

    • 2023-polyphosphate

      Public
      Sequence and structure homology of proteins involved in microbial polyphosphate cycling
      Jupyter Notebook
      •0•2•0•0•Updated Jul 6, 2026Jul 6, 2026

    • 2025-epistasis-dl-quantgen

      Public
      exploratory work with gpatlas datasets
      Jupyter Notebook
      •0•0•0•0•Updated Jul 6, 2026Jul 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 fam…
      Nextflow
      •
      GNU Affero General Public License v3.0
      •4•25•20•1•Updated Jul 6, 2026Jul 6, 2026

    • 2025_genopheno_local_linear_mapping

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 6, 2026Jul 6, 2026

    • 2025-gnn-evo-architecture

      Public
      Graph Neural Networks: A unifying predictive model architecture for evolutionary applications
      R
      •
      MIT License
      •0•5•0•0•Updated Jul 6, 2026Jul 6, 2026

    • glass-box-umap-notebook-pub

      Public
      Exact feature attribution with UMAP
      Jupyter Notebook
      •
      MIT License
      •3•17•1•0•Updated Jul 6, 2026Jul 6, 2026

    • 2025-diyraman-bio

      Public
      Repository associated with the 2025 DIY Raman spectroscopy for biological research pub
      spectroscopyspectral-analysisraman
      spectroscopyspectral-analysisraman
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Jul 6, 2026Jul 6, 2026

    • 2026-spombe-dataset

      Public template
      Code for 2026 S. pombe dataset pub
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 5, 2026Jul 5, 2026

    • microchamber-analysis

      Public template
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2026Jun 29, 2026

    • agar-microchamber

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 29, 2026Jun 29, 2026

    • 2025-raman-spectrometer-comparison

      Public
      Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"
      Jupyter Notebook
      •
      MIT License
      •1•1•1•1•Updated Jun 29, 2026Jun 29, 2026

    • sam3

      Public
      The repository provides code for running inference and finetuning with the Meta Segment Anything Model 3 (SAM 3), links for downloading the trained model checkp…
      Python
      •
      Other
      •1.7k•0•0•0•Updated Jun 24, 2026Jun 24, 2026

    • 2025-phylogenetic-analysis-of-msa-pairformer

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 23, 2026Jun 23, 2026

    • 2025-asr-plms

      Public
      Exploring the intersection of Ancestral Sequence Reconstruction, Protein Language Models, and Consensus Bias
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • glass-box-umap

      Public
      Python package for making UMAP interpretable with exact feature contributions
      Python
      •
      MIT License
      •2•50•4•0•Updated Jun 23, 2026Jun 23, 2026

    • chlamy-comparison

      Public template
      This repository contains code for image processing and analysis to compare phenotypes of interfertile algal species.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 22, 2026Jun 22, 2026

    • 2025-phylogenies-and-bfms

      Public
      R
      •
      MIT License
      •0•2•0•0•Updated Jun 22, 2026Jun 22, 2026

    • accounting-for-nonlinear-phenotypes

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Jun 22, 2026Jun 22, 2026

    • comparative-amoeboid-crawling

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 22, 2026Jun 22, 2026

    • 2025-Asgard-giant-virus-proteomes

      Public template
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • raman-taxonomy

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jun 22, 2026Jun 22, 2026

    • 2025-asgard-ncldv-OG-diversity

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jun 22, 2026Jun 22, 2026

    • 2025-GFP-variant-design

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•1•Updated Jun 22, 2026Jun 22, 2026

    • 2024-organismal-selection

      Public
      Code associated with the pub "Leveraging evolution to identify novel organismal models of human biology"
      R
      •
      MIT License
      •0•0•0•1•Updated Jun 22, 2026Jun 22, 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)
      Python
      •
      MIT License
      •14•82•2•0•Updated Jun 11, 2026Jun 11, 2026

    • cayman-his-elisa-opentrons-workflow

      Public
      An Opentrons OT-2 workflow for Cayman Chemical His-tag detection ELISA kit
      Jupyter Notebook
      •
      MIT License
      •1•1•4•0•Updated Jun 10, 2026Jun 10, 2026
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