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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 60 20

  2. amn_release amn_release Public

    Jupyter Notebook 19 7

  3. rp2paths rp2paths Public

    RetroPath2.0 to pathways

    Python 18 10

  4. active_learning_cell_free active_learning_cell_free Public

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

    Jupyter Notebook 14 12

  5. retropath2-wrapper retropath2-wrapper Public

    Python wrapper for Retropath2.0 Knime workflow

    JavaScript 10 1

  6. neo4jsbml neo4jsbml Public

    Bridge the gap between SBML data and Neo4j

    Python 8

Repositories

Showing 10 of 101 repositories
  • brsynth/selenzy-wrapper's past year of commit activity
    Python 2 MIT 0 0 1 Updated Oct 21, 2026
  • rplibs Public

    Libraries for rpTools

    Python 0 MIT 0 0 0 Updated Oct 21, 2026
  • galaxytools Public

    Galaxy wrappers of SynBioCAD tools suite

    brsynth/galaxytools's past year of commit activity
    HTML 2 MIT 0 0 3 Updated Oct 21, 2026
  • rptools-feedstock Public Forked from conda-forge/rptools-feedstock

    A conda-smithy repository for rptools.

    brsynth/rptools-feedstock's past year of commit activity
    0 BSD-3-Clause 5 0 0 Updated Oct 20, 2026
  • rptools Public

    Suite of tools that work on rpSBML format

    brsynth/rptools's past year of commit activity
    HTML 7 MIT 2 6 2 Updated Oct 20, 2026
  • rpCompletion Public

    Mono-component reactions completion

    brsynth/rpCompletion's past year of commit activity
    Python 2 MIT 2 0 0 Updated Oct 17, 2026
  • rr_cache Public

    RetroRules Cache

    brsynth/rr_cache's past year of commit activity
    Python 0 MIT 1 0 0 Updated Oct 16, 2026
  • rpScore Public

    Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, FBA and thermodynamics metrics, and the number of reactions in the pathway.

    brsynth/rpScore's past year of commit activity
    Python 0 MIT 1 0 0 Updated Oct 16, 2026
  • BioBot Public
    brsynth/BioBot's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 16, 2026
  • RRParser Public

    Reaction rules parser

    brsynth/RRParser's past year of commit activity
    Python 2 MIT 0 0 0 Updated Oct 14, 2026

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