Enveda

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32 repositories

DreaMS-Enveda
Public archive
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS (Nat Biotechnology)
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Mar 4, 2026Mar 4, 2026
computational-metabolomics-review
Public
Trends in Computational Metabolomics (2021–2025)
awesome bioinformatics awesome-list
awesome bioinformatics awesome-list metabolomics omics computational-metabolomics
Jupyter Notebook
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GNU General Public License v3.0
•2•12•0•0•Updated Feb 13, 2026Feb 13, 2026
np-clinical-trials
Public
Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"
drug-discovery clinical-trials natural-products
drug-discovery clinical-trials natural-products
Jupyter Notebook
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GNU General Public License v3.0
•1•3•0•8•Updated Feb 4, 2026Feb 4, 2026
NMR-Networking
Public
HSQC Molecular Networking Code for Publication
Python
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Other
•1•1•0•1•Updated Feb 2, 2026Feb 2, 2026
weighting-spectral-similarity
Public
Scripts and notebooks from Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation
mass-spectrometry
mass-spectrometry
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•2•0•7•Updated Dec 16, 2025Dec 16, 2025
spec2tax
Public
repo to support the spec2tax poster at ASMS 2022
Jupyter Notebook
•0•1•0•1•Updated Dec 16, 2025Dec 16, 2025
sparc-multiomics
Public
SPARC CCF Multi-omics analysis
machine-learning ibd biomarker-discovery
machine-learning ibd biomarker-discovery precision-medicine inflammatory-bowel-disease patient-stratification
Jupyter Notebook
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GNU General Public License v2.0
•2•3•0•1•Updated Dec 16, 2025Dec 16, 2025
sinusoidal-embedding
Public
code to generate sinusoidal embeddings
Python
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GNU General Public License v2.0
•1•2•0•4•Updated Dec 16, 2025Dec 16, 2025
modbioterp-enveda
Public
Jupyter Notebook
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GNU General Public License v2.0
•0•0•0•3•Updated Dec 16, 2025Dec 16, 2025
chemical-space-estimation
Public
Scripts and notebooks for Defining the limits of plant chemical space: challenges and estimations
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•2•Updated Dec 16, 2025Dec 16, 2025
ccs-prediction
Public
Evaluating the generalizability of graph neural networks for predicting collision cross section
deep-learning mass-spectrometry collision-cross-section
deep-learning mass-spectrometry collision-cross-section gnn
Jupyter Notebook
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GNU General Public License v2.0
•2•3•0•1•Updated Dec 16, 2025Dec 16, 2025
ccf-medication
Public
A biomarker catalog for inflammatory bowel disease medications
Jupyter Notebook
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GNU General Public License v2.0
•0•0•0•1•Updated Dec 16, 2025Dec 16, 2025
OctoCAT_Supply
Public
Python
•1•0•0•0•Updated Dec 4, 2025Dec 4, 2025
mspaint
Public
multi-engine painting of mass spec data
Jupyter Notebook
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GNU General Public License v2.0
•0•0•6•2•Updated Aug 18, 2025Aug 18, 2025
alphatims
Public
An open-source Python package for efficient accession and visualization of Bruker TimsTOF raw data from the Mann Labs at the Max Planck Institute of Biochemistr…
Python
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Apache License 2.0
•29•0•0•1•Updated Apr 18, 2025Apr 18, 2025
tIFAr
Public
R
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 6, 2024Nov 6, 2024
RPath
Public archive
Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"
knowledge-graph drug-discovery transcriptomics
knowledge-graph drug-discovery transcriptomics network-biology causal-networks mechanism-of-action
Jupyter Notebook
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Other
•5•19•0•0•Updated Jul 3, 2024Jul 3, 2024
plant-chemical-space
Public
Source code and data for "Exploring the known chemical space of the plant kingdom: Insights into taxonomic patterns, knowledge gaps, and bioactive regions"
cheminformatics computational-biology drug-discovery
cheminformatics computational-biology drug-discovery natural-products approved-drugs bioactivity
Jupyter Notebook
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GNU General Public License v2.0
•2•2•0•2•Updated Jun 18, 2024Jun 18, 2024
kgem-ensembles-in-drug-discovery
Public
Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"
machine-learning knowledge-graph drug-discovery
machine-learning knowledge-graph drug-discovery ensemble-model kgem
Jupyter Notebook
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Other
•4•20•0•0•Updated Jan 17, 2024Jan 17, 2024
ethnobotany
Public
Source code and data for "Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses…
data-science bioinformatics cheminformatics
data-science bioinformatics cheminformatics computational-biology drug-discovery ethnobotany
Jupyter Notebook
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GNU General Public License v2.0
•2•3•0•0•Updated Sep 5, 2023Sep 5, 2023
transcriptomic-target-correlation
Public
On the correspondence between the transcriptomic response of a compound and its targets
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•1•0•1•Updated Jul 6, 2023Jul 6, 2023
sapbert
Public
[NAACL & ACL 2021] SapBERT: Self-alignment pretraining for BERT & XL-BEL: Cross-Lingual Biomedical Entity Linking.
Python
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MIT License
•39•0•0•2•Updated Jun 12, 2023Jun 12, 2023
timsconvert
Public archive
Python
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Apache License 2.0
•23•0•0•0•Updated Apr 5, 2023Apr 5, 2023
deconv_benchmark
Public
R
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Other
•20•0•0•0•Updated Oct 25, 2022Oct 25, 2022
hgraph2graph
Public
Hierarchical Generation of Molecular Graphs using Structural Motifs
Python
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MIT License
•127•1•0•0•Updated Oct 10, 2022Oct 10, 2022
nbdev-demo
Public archive
Demonstration of nbdev-based development
Jupyter Notebook
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Apache License 2.0
•0•0•0•0•Updated Sep 8, 2022Sep 8, 2022
biomedical-nlp-datasets
Public
Tools for curating biomedical training data for large-scale language modeling
Python
•119•0•0•0•Updated Jun 24, 2022Jun 24, 2022
commonMZ
Public
A collection of common mz values found in mass spectrometry.
R
•8•0•0•0•Updated Jun 22, 2022Jun 22, 2022
misosoup-preview
Public archive
Farm-to-Table Mass-Spec Data Processing
Jupyter Notebook
•0•1•0•0•Updated Jun 9, 2022Jun 9, 2022
GenBioEL
Public
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning[NAACL 2022]
Python
•6•0•0•0•Updated Jun 3, 2022Jun 3, 2022