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    24 repositories

    • alphafast

      Public
      AlphaFast: ultra-high-throughput AlphaFold3 inference with MMSeqs2-GPU
      Python
      •
      Other
      •13•125•3•0•Updated Apr 11, 2026Apr 11, 2026

    • PRISM_Rebuttal

      Public
      0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • RLXF

      Public
      Consolidated repository to perform RLXF
      Python
      •
      Apache License 2.0
      •1•40•0•0•Updated Mar 12, 2026Mar 12, 2026

    • omega

      Public
      OMEGA code described in "Scalable and cost-efficient custom gene library assembly from oligopools."
      Python
      •
      GNU General Public License v3.0
      •12•37•1•0•Updated Nov 18, 2025Nov 18, 2025

    • scalable-gene-assembly

      Public
      Data analysis and figures for OMEGA publication.
      Jupyter Notebook
      •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • METL_Rosetta

      Public
      Repo with command line and PyRosetta code to compute a JSON dictionary containing two-body and one-body energy terms for a given model system
      Python
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • finetuning_esm2

      Public
      Setting up generalizable repository to finetune esm2 models
      Python
      •
      MIT License
      •0•4•0•0•Updated Apr 1, 2025Apr 1, 2025

    • nn-extrapolation

      Public
      Neural network extrapolation to distant regions of the protein fitness landscape
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Jun 24, 2024Jun 24, 2024

    • nn4dms_nn-extrapolate

      Public
      Neural networks for deep mutational scanning data
      Jupyter Notebook
      •
      MIT License
      •18•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • nn-extrapolation-models

      Public
      Pretrained models used in nn-extrapolation.
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • ML-Guided-Acyl-ACP-Reductase-Engineering

      Public
      Repository containing scripts and analysis for ML-Guided Acyl-ACP Reductase Engineering paper
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•11•2•0•Updated Nov 21, 2023Nov 21, 2023

    • SAMPLE_code

      Public
      Jupyter Notebook
      •1•6•0•0•Updated Oct 27, 2023Oct 27, 2023

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.6k•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • tutorials

      Public
      Romero lab tutorials and information for lab server and GitHub usage.
      0•0•0•0•Updated Sep 8, 2023Sep 8, 2023

    • schemarecomb

      Public
      Design chimeric protein libraries with Golden Gate Assembly.
      pythonbioinformaticsprotein
      pythonbioinformaticsproteinprotein-design
      Python
      •
      GNU General Public License v3.0
      •5•7•0•1•Updated Jul 8, 2023Jul 8, 2023

    • dhfr_neutral_evolution

      Public
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated Feb 8, 2023Feb 8, 2023

    • Seq2FxnNN

      Public
      Example for training a neural network to predict functional scores from sequence inputs
      Jupyter Notebook
      •1•0•0•0•Updated Jan 31, 2023Jan 31, 2023

    • DMS-analysis

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jan 24, 2023Jan 24, 2023

    • microfluidic-designs

      Public
      Blueprints to fabricate microfluidic devices found in various papers
      DataWeave
      •0•0•0•0•Updated Apr 12, 2021Apr 12, 2021

    • PU-learning-paper-analysis

      Public
      Data and analysis scripts for the PU learning paper
      PostScript
      •1•1•0•0•Updated Feb 6, 2021Feb 6, 2021

    • pudms

      Public
      positive-unlabeled learning for dms datasets
      R
      •3•3•0•0•Updated Dec 29, 2020Dec 29, 2020

    • syringe-pump-controller

      Public
      Python GUI to operate New Era syringe pumps
      Python
      •
      GNU Lesser General Public License v3.0
      •1•5•0•0•Updated Sep 10, 2019Sep 10, 2019

    • seq-fcn-data

      Public
      Protein sequence-function data sets
      Python
      •0•2•0•0•Updated May 14, 2018May 14, 2018

    • protovitro

      Public
      software tools for designing informative sets of sequences from metagenomic data
      Python
      •0•2•0•0•Updated Nov 15, 2017Nov 15, 2017
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