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36 repositories

adaptyvbio-nipah
Public
Adaptyv Nipah Binder Competition
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Mar 20, 2026Mar 20, 2026
metl
Public
Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models
Python
•
MIT License
•10•62•2•1•Updated Feb 3, 2026Feb 3, 2026
tps
Public
Temporal Pathway Synthesizer
Jupyter Notebook
•
Other
•8•0•0•1•Updated Oct 10, 2025Oct 10, 2025
metl-sim
Public
High-throughput framework for running molecular simulations for METL
Python
•
MIT License
•6•22•4•0•Updated Sep 18, 2025Sep 18, 2025
metl-pub
Public
Supplementary datasets and scripts for the METL manuscript
Jupyter Notebook
•
MIT License
•1•9•0•0•Updated Sep 18, 2025Sep 18, 2025
metl-pretrained
Public
Pretrained METL models with minimal dependencies
Python
•
MIT License
•5•17•1•1•Updated Sep 18, 2025Sep 18, 2025
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•3•0•0•Updated Sep 14, 2025Sep 14, 2025
ChemLML
Public
Chemical Language Model Linker
Python
•
MIT License
•1•8•2•0•Updated Aug 22, 2025Aug 22, 2025
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 Aug 8, 2025Aug 8, 2025
active-learning-drug-discovery
Public
Iterative chemical screening pipeline for drug discovery
drug-discovery active-learning virtual-screening
drug-discovery active-learning virtual-screening
Jupyter Notebook
•
MIT License
•0•6•13•1•Updated Aug 6, 2025Aug 6, 2025
Assay2Mol
Public
Python
•
MIT License
•0•2•0•0•Updated Jul 31, 2025Jul 31, 2025
nn4dms
Public
Neural networks for deep mutational scanning data
Jupyter Notebook
•
MIT License
•18•72•0•0•Updated May 30, 2025May 30, 2025
ml4bio
Public
A graphical interface for sklearn classification to introduce machine learning to biologists
education machine-learning
education machine-learning
Python
•
MIT License
•3•14•21•1•Updated Mar 19, 2025Mar 19, 2025
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
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•26•0•Updated Aug 30, 2024Aug 30, 2024
SINGE
Public
Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
regulatory-network single-cell-rna-seq granger-causality
regulatory-network single-cell-rna-seq granger-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
pria-ams-enamine
Public
Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
machine-learning biochemistry virtual-screening
machine-learning biochemistry virtual-screening
Jupyter Notebook
•
MIT License
•1•7•0•0•Updated Sep 22, 2023Sep 22, 2023
rare-disease-network-analysis
Public
Network analysis of genetic variants
Jupyter Notebook
•
MIT License
•0•1•2•0•Updated Aug 31, 2023Aug 31, 2023
bds-srop-demo-manuscript
Public
Demo manubot manuscript for BDS SROP students
HTML
•
Creative Commons Attribution 4.0 International
•5•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
ssps
Public
Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
probabilistic-programming gen signaling-pathway
probabilistic-programming gen signaling-pathway dynamic-bayesian-network
Julia
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MIT License
•0•14•0•0•Updated Oct 24, 2022Oct 24, 2022
pathway-parameter-advising
Public
Parameter advising for biological pathway creation algorithms
hyperparameter-tuning graphlet protein-protein-interaction-network
hyperparameter-tuning graphlet protein-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
SINGE-supplemental
Public
Supplemental scripts and analyses for the SINGE manuscript
regulatory-network single-cell-rna-seq granger-causality
regulatory-network single-cell-rna-seq granger-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.
education machine-learning
education machine-learning
HTML
•
Creative Commons Zero v1.0 Universal
•1•1•1•0•Updated Aug 20, 2021Aug 20, 2021
t-cell-classification
Public
Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow
jupyter-notebook image-classification transfer-learning
jupyter-notebook image-classification transfer-learning autofluorescence-microscopy
Jupyter Notebook
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BSD 3-Clause Clear License
•1•6•1•0•Updated Mar 22, 2021Mar 22, 2021

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Gitter Lab

All

All

36 repositories

adaptyvbio-nipah

metl

tps

metl-sim

metl-pub

metl-pretrained

benchmarking-structure-based-models

ChemLML

pathway-localization

active-learning-drug-discovery

Assay2Mol

nn4dms

ml4bio

hiv1-aurkb

min-cost-flow

low-n-mlde-review

SINGE

osmotic-stress

pria-ams-enamine

rare-disease-network-analysis

bds-srop-demo-manuscript

network-notebook-examples

influenza-pb2

ssps

pathway-parameter-advising

NetworkMeasures

SINGE-supplemental

test-notifications

ml-bio-workshop

t-cell-classification

All

All

Repositories list

36 repositories