Systems Biology at University of Michigan

All

20 repositories

emt-cobra
Public
Modeling the metabolic changes during the epithelial-to-mesenchymal transition.
bioinformatics constraint-based-modeling omics-data-integration
HTML
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GNU General Public License v3.0
•1•3•0•0•Updated Dec 7, 2024Dec 7, 2024
TACTIC
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Dec 2, 2024Dec 2, 2024
SCOOTI
Public
Single Cell Optimization Objective and Tradeoff Inference
Python
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Nov 24, 2024Nov 24, 2024
M2D2
Public
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 22, 2024Nov 22, 2024
CARAMeL
Public
Condition-specific Antibiotic Regimen Assessment using Mechanistic Learning
matlab
MATLAB
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GNU General Public License v3.0
•0•1•0•0•Updated Jul 24, 2024Jul 24, 2024
INDIGOpy
Public
Implementation of INDIGO (INferring Drug Interactions using chemoGenomics and Orthology) as a Python package.
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Jun 4, 2024Jun 4, 2024
quiescence-depth-modulation
Public
Leveraging Metabolic Modeling and Machine Learning to Uncover Modulators of Quiescence Depth
MATLAB
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GNU General Public License v3.0
•0•0•0•0•Updated Jan 19, 2024Jan 19, 2024
metoncofit-website
Public
A dashboard for the MetOncoFit tumor models.
flask website data-science dashboard exploratory-data-analysis plotly data-visualization python3 data-visualisation plotly-dash
Python
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MIT License
•1•0•0•3•Updated Dec 8, 2022Dec 8, 2022
met-ptm-drug-cancer
Public
Machine learning to learn metabolite-histone-drug interactions in cancer.
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Nov 19, 2022Nov 19, 2022
MetOncoFit
Public
Common biochemical and topological attributes of metabolic genes recurrently dysregulated in tumors.
machine-learning random-forest cancer-research metabolic-models genome-scale-models cancer-metabolism metabolic-network metabolic-attributes tumors tumor-models
HTML
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GNU General Public License v3.0
•6•1•10•11•Updated Sep 30, 2022Sep 30, 2022
egem
Public
epigenome scale metabolic modeling for cancer metabolism
metabolic-models metabolic-reconstruction epigenomics cancer-metabolism genome-scale-modeling histone-ptms histone-acetylation drug-sensitivity
MATLAB
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MIT License
•2•4•6•3•Updated Apr 16, 2022Apr 16, 2022
MAGENTA
Public
Metabolism And GENomics-based Tailoring of Antibiotic regimens: predicts the impact of pathogen environment on antibiotic potency based on chemogenomic data.
C++
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GNU General Public License v3.0
•1•1•0•0•Updated Mar 18, 2022Mar 18, 2022
bme499
Public
BME499 course materials
data-science ai random-forest matlab regression data-visualization neural-networks decision-trees unsupervised-learning hypothesis-testing
HTML
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MIT License
•1•1•0•0•Updated Mar 24, 2021Mar 24, 2021
single-cell-neutrophil-flux-analysis
Public
Analysis of neutrophil metabolic activity during metastasis using single-cell RNASeq and COnstraint-Based Reconstruction and Analysis.
flux-balance-analysis metastasis single-cell-analysis immunometabolism
HTML
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GNU General Public License v3.0
•2•0•0•0•Updated Mar 12, 2021Mar 12, 2021
metabolicmodeling
Public
Constraint-based metabolic modeling software from the Chandrasekaran Lab
python matlab constraint-based-modeling omics-data-integration fluxomics genome-scale-modeling
HTML
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GNU General Public License v3.0
•2•2•3•1•Updated Jan 28, 2021Jan 28, 2021
dfa
Public
Fitting time-course metabolomics onto genome-scale metabolic models for inferring metabolic activity.
matlab metabolomics cobra metabolic-models time-course
MATLAB
•1•1•0•0•Updated Sep 15, 2020Sep 15, 2020
astrix
Public
Using gene expression data to identify regulatory interactions between transcription factors and target genes.
MATLAB
•0•0•2•0•Updated May 23, 2020May 23, 2020
gemini
Public
Integrating the transcriptional regulatory network with genome-scale metabolic models.
matlab metabolism transcriptional-regulatory-network constraint-based-modeling genome-scale-modeling
MATLAB
•1•1•0•0•Updated May 23, 2020May 23, 2020
github-tutorials
Public
Another version control resource and tutorial repo
github git research version-control project-management tutorial github-tutorials
GNU General Public License v3.0
•0•0•3•0•Updated May 11, 2020May 11, 2020
docker-tutorials
Public
Another tutorial and resource for using docker to launch web applications
docker docker-tutorials
GNU General Public License v3.0
•0•0•0•0•Updated Jan 28, 2020Jan 28, 2020