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    27 repositories

    • modbioterp-enveda

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•2•Updated May 23, 2025May 23, 2025

    • chemical-space-estimation

      Public
      Scripts and notebooks for Defining the limits of plant chemical space: challenges and estimations
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•1•Updated May 23, 2025May 23, 2025

    • mspaint

      Public
      multi-engine painting of mass spec data
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•6•3•Updated May 22, 2025May 22, 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 Biochemistry.
      Python
      •
      Apache License 2.0
      •29•0•0•1•Updated Apr 18, 2025Apr 18, 2025

    • sparc-multiomics

      Public
      SPARC CCF Multi-omics analysis
      machine-learningibdbiomarker-discoveryprecision-medicineinflammatory-bowel-diseasepatient-stratification
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •1•3•0•0•Updated Jan 6, 2025Jan 6, 2025

    • tIFAr

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • ccs-prediction

      Public
      Evaluating the generalizability of graph neural networks for predicting collision cross section
      deep-learningmass-spectrometrycollision-cross-sectiongnn
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •2•3•0•0•Updated Oct 30, 2024Oct 30, 2024

    • np-clinical-trials

      Public
      Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"
      drug-discoveryclinical-trialsnatural-products
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•3•0•7•Updated Aug 9, 2024Aug 9, 2024

    • RPath

      Public
      Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"
      knowledge-graphdrug-discoverytranscriptomicsnetwork-biologycausal-networksmechanism-of-action
      Jupyter Notebook
      •
      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"
      cheminformaticscomputational-biologydrug-discoverynatural-productsapproved-drugsbioactivity
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •2•1•0•2•Updated Jun 18, 2024Jun 18, 2024

    • weighting-spectral-similarity

      Public
      Scripts and notebooks from Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation
      mass-spectrometry
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•6•Updated Jan 29, 2024Jan 29, 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-learningknowledge-graphdrug-discoveryensemble-modelkgem
      Jupyter Notebook
      •
      Other
      •4•20•0•0•Updated Jan 17, 2024Jan 17, 2024

    • sinusoidal-embedding

      Public
      code to generate sinusoidal embeddings
      Python
      •
      GNU General Public License v2.0
      •1•2•0•3•Updated Oct 17, 2023Oct 17, 2023

    • 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-sciencebioinformaticscheminformaticscomputational-biologydrug-discoveryethnobotany
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •1•2•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
      •
      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
      •
      MIT License
      •37•0•0•2•Updated Jun 12, 2023Jun 12, 2023

    • timsconvert

      Public archive
      Python
      •
      Apache License 2.0
      •19•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • deconv_benchmark

      Public
      R
      •
      Other
      •20•0•0•0•Updated Oct 25, 2022Oct 25, 2022

    • hgraph2graph

      Public
      Hierarchical Generation of Molecular Graphs using Structural Motifs
      Python
      •
      MIT License
      •114•0•0•0•Updated Oct 10, 2022Oct 10, 2022

    • nbdev-demo

      Public archive
      Demonstration of nbdev-based development
      Jupyter Notebook
      •
      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
      •116•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

    • spec2tax

      Public
      repo to support the spec2tax poster at ASMS 2022
      Jupyter Notebook
      •0•1•0•0•Updated Jun 5, 2022Jun 5, 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

    • libPeak

      Public archive
      Methods of peak detection for analytical instruments
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•0•0•0•Updated Oct 13, 2021Oct 13, 2021

    • biosaur_adapter

      Public archive
      Python
      •1•0•0•0•Updated Aug 16, 2021Aug 16, 2021