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    33 repositories

    • metl-sim

      Public
      High-throughput framework for running molecular simulations for METL
      Python
      •
      MIT License
      •4•10•2•1•Updated Dec 16, 2024Dec 16, 2024

    • metl-pub

      Public
      Supplementary datasets and scripts for the METL manuscript
      Python
      •
      MIT License
      •0•5•0•1•Updated Dec 13, 2024Dec 13, 2024

    • nn4dms

      Public
      Neural networks for deep mutational scanning data
      Jupyter Notebook
      •
      MIT License
      •17•66•0•0•Updated Nov 13, 2024Nov 13, 2024

    • ChemLML

      Public
      Chemical Language Model Linker
      Python
      •
      MIT License
      •1•3•2•0•Updated Nov 6, 2024Nov 6, 2024

    • metl-pretrained

      Public
      Pretrained METL models with minimal dependencies
      Python
      •
      MIT License
      •0•13•3•1•Updated Nov 5, 2024Nov 5, 2024

    • hiv1-aurkb

      Public
      Scripts for analyzing HIV-1 producer cell proteomic and phosphoproteomic data
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 31, 2024Oct 31, 2024

    • metl

      Public
      Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models
      Python
      •
      MIT License
      •3•24•1•1•Updated Oct 25, 2024Oct 25, 2024

    • benchmarking-structure-based-models

      Public
      This is a repository of code needed to replicate benchmarks of structure based models in ProteinGym
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 21, 2024Sep 21, 2024

    • min-cost-flow

      Public
      Pathway reconstruction with a minimum cost flow algorithm
      Python
      •
      MIT License
      •1•1•1•1•Updated Sep 18, 2024Sep 18, 2024

    • low-n-mlde-review

      Public
      Low N machine learning-assisted directed evolution perspective written with Manubot
      HTML
      •
      Creative Commons Attribution 4.0 International
      •0•0•2•0•Updated Aug 30, 2024Aug 30, 2024

    • SINGE

      Public
      Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
      regulatory-networksingle-cell-rna-seqgranger-causality
      MATLAB
      •
      MIT License
      •6•11•13•3•Updated Jul 11, 2024Jul 11, 2024

    • osmotic-stress

      Public
      A study of yeast osmotic stress response signaling
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

    • active-learning-drug-discovery

      Public
      End-to-end active learning pipeline for virtual screening and drug discovery
      Jupyter Notebook
      •
      MIT License
      •0•3•11•1•Updated Mar 7, 2024Mar 7, 2024

    • pria-ams-enamine

      Public
      Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
      machine-learningbiochemistryvirtual-screening
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated Sep 22, 2023Sep 22, 2023

    • bds-srop-demo-manuscript

      Public
      Demo manubot manuscript for BDS SROP students
      HTML
      •
      Creative Commons Attribution 4.0 International
      •6•0•0•0•Updated Jul 25, 2023Jul 25, 2023

    • network-notebook-examples

      Public
      Test pandas and networkx in Jupyter notebooks
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 7, 2023Jun 7, 2023

    • influenza-pb2

      Public
      Analysis of influenza PB2 protein interactions
      Python
      •
      MIT License
      •1•0•2•0•Updated Dec 24, 2022Dec 24, 2022

    • pathway-localization

      Public
      Scripts, data, and supplementary information for "Graph algorithms for predicting subcellular localization at the pathway level"
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•1•1•0•Updated Dec 14, 2022Dec 14, 2022

    • ssps

      Public
      Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
      probabilistic-programminggensignaling-pathwaydynamic-bayesian-network
      Julia
      •
      MIT License
      •0•14•0•0•Updated Oct 24, 2022Oct 24, 2022

    • ml4bio

      Public
      A graphical interface for sklearn classification to introduce machine learning to biologists
      educationmachine-learning
      Python
      •
      MIT License
      •3•11•20•2•Updated Oct 11, 2022Oct 11, 2022

    • pathway-parameter-advising

      Public
      Parameter advising for biological pathway creation algorithms
      hyperparameter-tuninggraphletprotein-protein-interaction-network
      Python
      •
      MIT License
      •0•3•3•0•Updated Sep 7, 2022Sep 7, 2022

    • NetworkMeasures

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • tps

      Public
      Temporal Pathway Synthesizer
      Python
      •
      Other
      •8•0•0•1•Updated Jul 7, 2022Jul 7, 2022

    • SINGE-supplemental

      Public
      Supplemental scripts and analyses for the SINGE manuscript
      regulatory-networksingle-cell-rna-seqgranger-causality
      MATLAB
      •
      MIT License
      •1•1•0•0•Updated May 7, 2022May 7, 2022

    • test-notifications

      Public
      Test repo for notification integration
      Creative Commons Zero v1.0 Universal
      •0•0•1•0•Updated Aug 26, 2021Aug 26, 2021

    • ml-bio-workshop

      Public
      Former repository for the Machine Learning for Biology workshop. Moved to https://github.com/carpentries-incubator/ml4bio-workshop.
      educationmachine-learning
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •1•0•1•0•Updated Aug 20, 2021Aug 20, 2021

    • t-cell-classification

      Public
      Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow
      jupyter-notebookimage-classificationtransfer-learningautofluorescence-microscopy
      Jupyter Notebook
      •
      BSD 3-Clause Clear License
      •2•6•1•0•Updated Mar 22, 2021Mar 22, 2021

    • pharmaco-image

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•11•0•Updated Aug 10, 2020Aug 10, 2020

    • LPWC

      Public
      Lag Penalized Weighted Correlation for Time Series Clustering
      bioinformaticstime-seriesclustering
      R
      •
      Other
      •3•20•5•0•Updated Apr 25, 2020Apr 25, 2020

    • prmf

      Public
      Pathway-Regularized Matrix Factorization
      Python
      •
      MIT License
      •0•12•6•0•Updated Apr 6, 2020Apr 6, 2020