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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

  1. RetroPathRL RetroPathRL Public

    Reinforcement Learning based bioretrosynthesis tool

    Python 47 16

  2. rp2paths rp2paths Public

    RetroPath2.0 to pathways

    Python 15 9

  3. active_learning_cell_free active_learning_cell_free Public

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

    Jupyter Notebook 10 11

  4. RetroPath2-wrapper RetroPath2-wrapper Public

    Python wrapper for Retropath2.0 Knime workflow

    JavaScript 7 1

  5. rptools rptools Public

    Suite of tools that work on rpSBML format

    HTML 6 2

  6. amn_release amn_release Public

    Jupyter Notebook 6 4

Repositories

Showing 10 of 79 repositories
  • brsynth/extractor_brendapy’s past year of commit activity
    Python 0 0 0 0 Updated Jun 20, 2024
  • RetroPathRL Public

    Reinforcement Learning based bioretrosynthesis tool

    brsynth/RetroPathRL’s past year of commit activity
    Python 47 MIT 16 0 0 Updated Jun 20, 2024
  • icfree-ml Public

    Design of experiments (DoE) and machine learning packages for the iCFree project

    brsynth/icfree-ml’s past year of commit activity
    Python 4 MIT 2 1 0 Updated Jun 19, 2024
  • galaxytools Public

    Galaxy wrappers of SynBioCAD tools suite

    brsynth/galaxytools’s past year of commit activity
    HTML 0 MIT 0 3 6 Updated Jun 18, 2024
  • brsynth/amn_release’s past year of commit activity
    Jupyter Notebook 6 MIT 4 3 1 Updated May 8, 2024
  • straindesign Public

    Library to perform metabolic engineering tasks

    brsynth/straindesign’s past year of commit activity
    Python 4 MIT 0 2 1 Updated Apr 29, 2024
  • neo4jsbml Public

    Bridge the gap between SBML data and Neo4j

    brsynth/neo4jsbml’s past year of commit activity
    Python 4 MIT 0 0 2 Updated Apr 29, 2024
  • brendapy Public Forked from matthiaskoenig/brendapy

    BRENDA parser in python

    brsynth/brendapy’s past year of commit activity
    Python 0 LGPL-3.0 6 0 0 Updated Mar 18, 2024
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    brsynth/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,124 0 0 Updated Mar 5, 2024
  • rptools Public

    Suite of tools that work on rpSBML format

    brsynth/rptools’s past year of commit activity
    HTML 6 MIT 2 4 1 Updated Mar 5, 2024

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