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BioRetroSynth

Our group is interested in synthetic biology and systems metabolic engineering in whole-cell and cell-free systems.

Bio-RetroSynth

Bio-RetroSynth group

Our group is interested in synthetic biology in whole-cell and cell-free systems. We develop computational and wet lab protocols to search, design, and engineer biological pathways and networks. Other activities include structure-activity, sequence-function relationships, retrosynthesis, and the design of experiments using active and reinforcement machine learning methods. The applications of our work include synthetic metabolic pathways and genetic circuits engineering for bioproduction, biosensing, and biocomputing.

Popular repositories Loading

  1. RetroPathRL RetroPathRL Public

    Reinforcement Learning based bioretrosynthesis tool

    Python 50 18

  2. rp2paths rp2paths Public

    RetroPath2.0 to pathways

    Python 18 10

  3. active_learning_cell_free active_learning_cell_free Public

    Scripts to perform active learning as described in the referenced article.

    Jupyter Notebook 13 12

  4. amn_release amn_release Public

    Jupyter Notebook 13 5

  5. RetroPath2-wrapper RetroPath2-wrapper Public

    Python wrapper for Retropath2.0 Knime workflow

    JavaScript 8 1

  6. rptools rptools Public

    Suite of tools that work on rpSBML format

    HTML 7 2

Repositories

Showing 10 of 86 repositories
  • rptools Public

    Suite of tools that work on rpSBML format

    brsynth/rptools’s past year of commit activity
    HTML 7 MIT 2 4 2 Updated Jul 30, 2025
  • rr_cache Public

    RetroRules Cache

    brsynth/rr_cache’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 30, 2025
  • dAMN Public

    New hybrid machine learning model combining artificial neural network and a dynamic flux balance analysis on a metabolic model to predict bacterial growth curve.

    brsynth/dAMN’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 30, 2025
  • rxn_rebuild Public

    Rebuild full reaction from reaction rule

    brsynth/rxn_rebuild’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Jul 28, 2025
  • PINN-v2 Public

    This repository contains a hybrid model based on the Physics-Informed Neural Network (PINN) framework, which integrates neural networks with ordinary differential equations (ODEs) to incorporate biological constraints into machine learning.

    brsynth/PINN-v2’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 27, 2025
  • rp2paths Public

    RetroPath2.0 to pathways

    brsynth/rp2paths’s past year of commit activity
    Python 18 MIT 10 0 0 Updated Jul 24, 2025
  • galaxytools Public

    Galaxy wrappers of SynBioCAD tools suite

    brsynth/galaxytools’s past year of commit activity
    HTML 0 MIT 0 0 1 Updated Jul 23, 2025
  • molecule-signature-paper Public

    Code supporting the paper 'Getting Molecules from their Fingerprints: Generative Models vs. Deterministic Enumeration'

    brsynth/molecule-signature-paper’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jun 18, 2025
  • molecule-signature Public

    Signature based molecule enumeration from morgan fingerprints

    brsynth/molecule-signature’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jun 17, 2025
  • chebirgroup Public

    Systematic expansion of R-group for ChEBI molecules from the RHEA database

    brsynth/chebirgroup’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jun 13, 2025

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