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    29 repositories

    • DeepMol

      Public
      DeepMol: A Machine and Deep Learning Framework for Computational Chemistry
      machine-learningdeep-learningchemoinformatics
      Python
      •
      BSD 2-Clause "Simplified" License
      •16•161•15•1•Updated Oct 10, 2025Oct 10, 2025

    • PredInhib-MTB

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jul 11, 2025Jul 11, 2025

    • ReactEA

      Public
      ReactEA: Combining Evolutionary Algorithms With Reaction Rules Towards Focused Molecular Design
      evolutionary-algorithmsdrug-discoveryreaction-rules
      Python
      •
      GNU General Public License v3.0
      •2•8•2•0•Updated Jul 2, 2025Jul 2, 2025

    • drug_response_pipeline

      Public
      Python
      •
      MIT License
      •1•7•1•0•Updated Jun 9, 2025Jun 9, 2025

    • BioCatalyzer

      Public
      BioCatalyzer: a rule-based tool to predict compound metabolism
      cheminformaticsmetabolismchemoinformaticsreaction-rulesenzymatic-reactions
      Python
      •
      MIT License
      •0•7•1•0•Updated May 28, 2025May 28, 2025

    • diel_models

      Public
      Tool to convert generic plant GEMs to diel plant GEMs
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 6, 2025Mar 6, 2025

    • deepmol_case_studies

      Public
      Case Studies from the DeepMol Publication
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•9•0•0•Updated Jan 23, 2025Jan 23, 2025

    • troppo

      Public
      Reconstruction algorithms for Python
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •8•26•7•3•Updated Oct 23, 2024Oct 23, 2024

    • BioCatalyzer-CaseStudy

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • MEWpy

      Public
      Metabolic Engineering Workbench
      pythonsimulationoptimizationmodelingmicrobial-communitiesstrainkinetic-modelingomics-data-integration
      Python
      •
      GNU General Public License v3.0
      •12•40•7•0•Updated Jun 9, 2024Jun 9, 2024

    • biomeneco

      Public
      A project to accelerate gap-filling of metabolic models
      MIT License
      •0•1•0•1•Updated Dec 5, 2023Dec 5, 2023

    • propythia

      Public
      Python generic modular semi-automated platform containing functions for the classification of proteins based on their physicochemical properties using ML.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •10•33•0•2•Updated Sep 4, 2023Sep 4, 2023

    • cobamp

      Public
      Constraint-based modeling framework for the enumeration of pathway analysis concepts
      fluxanalysismodelelementarymodespathwaymetabolicconstraint-based
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•14•3•2•Updated Jul 6, 2023Jul 6, 2023

    • biotmpy

      Public
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Jun 28, 2023Jun 28, 2023

    • bRNAsPipe

      Public
      Pipeline for RNAseq analysis in Bash and scripts for microarray gene expression analysis in R
      R
      •0•1•0•0•Updated May 31, 2023May 31, 2023

    • epigen

      Public
      Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer
      Python
      •0•0•1•0•Updated May 29, 2023May 29, 2023

    • BioISO

      Public
      Python
      •0•0•0•0•Updated Dec 7, 2022Dec 7, 2022

    • DeepSweet

      Public
      A Machine and Deep Learning pipeline to classify sweetness
      pythonmachine-learningdeep-learningcnndnnrnnchemoinformatics
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Jul 25, 2022Jul 25, 2022

    • merlinv4_paper

      Public
      Models analysis for merlin's version 4 submission on Nucleic Acid Research
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jul 6, 2022Jul 6, 2022

    • bit-analysis

      Public
      BiGG Integration Tool Analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 22, 2022Feb 22, 2022

    • onmtreaction

      Public
      Python
      •0•0•0•0•Updated Jan 12, 2022Jan 12, 2022

    • lab_models

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 9, 2021Nov 9, 2021

    • human_ts_models

      Public
      A repository for tissue-specific model reconstructions using troppo
      Jupyter Notebook
      •1•1•0•0•Updated Oct 28, 2021Oct 28, 2021

    • transyt

      Public
      Java
      •0•0•0•0•Updated Oct 20, 2021Oct 20, 2021

    • specmine

      Public
      R
      •1•4•0•0•Updated Sep 21, 2021Sep 21, 2021

    • cobamp-grasp

      Public
      A cobamp-dependent framework enabling gene regulatory and signalling pathway integration in metabolic models
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 6, 2021May 6, 2021

    • specmine.datasets

      Public
      A repository for the datasets used in R package specmine
      R
      •0•0•0•0•Updated Feb 17, 2021Feb 17, 2021

    • biosynth-framework

      Public
      Java
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Sep 4, 2020Sep 4, 2020

    • optimModels

      Public
      Framework to optimize metabolic models using evolutionary computation.
      Python
      •
      Other
      •2•2•0•0•Updated Apr 15, 2019Apr 15, 2019