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    20 repositories

    • hermes

      Public
      Python
      •
      MIT License
      •1•10•0•0•Updated Mar 31, 2026Mar 31, 2026

    • designimmune

      Public
      Studying information transmission in the adaptive immune response
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • foundry

      Public
      Central repository for biomolecular foundation models with shared trainers and pipeline components
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •132•1•0•0•Updated Jan 23, 2026Jan 23, 2026

    • hermes_experiments

      Public
      code, data and results of experiments shown in the HERMES paper
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 19, 2026Jan 19, 2026

    • tcr_antigen_design

      Public
      Jupyter Notebook
      •0•13•1•0•Updated May 19, 2025May 19, 2025

    • hpacker

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • Holographic-VAE

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • biophysics

      Public
      Jupyter Notebook
      •2•2•0•0•Updated Apr 7, 2025Apr 7, 2025

    • zernikegrams

      Public
      Stand-alone library for protein preprocessing
      Python
      •
      MIT License
      •0•2•1•0•Updated Feb 14, 2025Feb 14, 2025

    • protein_biophysics

      Public
      Collection of biophysical tools for manipulating proteins (e.g. pyrosetta)
      Python
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • protein_holography

      Public
      Code for holographic machine learning of proteins
      HTML
      •
      MIT License
      •4•25•1•2•Updated Oct 29, 2024Oct 29, 2024

    • dssp

      Public
      Application to assign secondary structure to proteins
      C++
      •
      BSD 2-Clause "Simplified" License
      •30•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • protein_holography-web

      Public
      Python
      •0•5•0•0•Updated Oct 2, 2024Oct 2, 2024

    • ProteinMPNN-finetuning

      Public
      Code for the ProteinMPNN paper + fine-tuning functionalities
      Jupyter Notebook
      •
      MIT License
      •451•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • Working_memory

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 7, 2021Dec 7, 2021

    • Tomoko

      Public
      Forward time simulator of genotypic evolution and fitness inference
      Julia
      •
      MIT License
      •0•1•0•0•Updated Dec 1, 2021Dec 1, 2021

    • HIVTreatmentOptimization

      Public
      Analysis of untreated patient sequences and viremia data for the purposes of optimizing passive-transfer bNAb therapy
      Mathematica
      •0•2•0•0•Updated Nov 24, 2021Nov 24, 2021

    • EscapeSimulator

      Public
      Simulate the escape dynamics of HIV-1 against all your favorite antibody combinations
      Julia
      •
      MIT License
      •0•1•0•0•Updated Nov 17, 2021Nov 17, 2021

    • ImmuneMemoryDM

      Public
      analysis for Optimal evolutionary decision-making to store immune memory
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 10, 2021May 10, 2021

    • covid-bcr

      Public
      Analysis of BCR repertoires from covid-19 infections
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Mar 19, 2021Mar 19, 2021
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