Repositories list

• reservoir

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 19, 2025Sep 19, 2025

• active_learning_cell_free

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

  Jupyter Notebook

  •12•13•0•0•Updated Sep 17, 2025Sep 17, 2025

• Bayesian-Experimental-Design-BED-

  Public
  Python

  •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

• galaxytools

  Public
  Galaxy wrappers of SynBioCAD tools suite

  synthetic-biologysystems-biologygalaxy-project

  HTML

  •

  MIT License

  •0•0•0•3•Updated Sep 15, 2025Sep 15, 2025

• rr_cache

  Public
  RetroRules Cache

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 12, 2025Sep 12, 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.

  Jupyter Notebook

  •1•0•0•0•Updated Sep 12, 2025Sep 12, 2025

• rxn_rebuild

  Public
  Rebuild full reaction from reaction rule

  Python

  •

  MIT License

  •0•2•0•0•Updated Sep 11, 2025Sep 11, 2025

• rptools

  Public
  Suite of tools that work on rpSBML format

  synthetic-biologysystems-biologysynbio+ 1metabolic-engineering

  HTML

  •

  MIT License

  •2•7•4•1•Updated Sep 11, 2025Sep 11, 2025

• biorgroup

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

  r-groupchebirhea

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025

• RetroPath2-wrapper

  Public
  Python wrapper for Retropath2.0 Knime workflow

  synthetic-biologysynbiometabolic-engineering

  JavaScript

  •

  MIT License

  •1•8•3•0•Updated Aug 21, 2025Aug 21, 2025

• molecule-signature-paper

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

  chemistrysignaturefingerprint+ 4generative-modelchemoinformaticsmolecular-generationdeterministic-enumeration

  Jupyter Notebook

  •

  MIT License

  •0•0•0•1•Updated Aug 12, 2025Aug 12, 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.

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• rp2paths

  Public
  RetroPath2.0 to pathways

  synthetic-biologysynbio

  Python

  •

  MIT License

  •10•18•0•0•Updated Jul 24, 2025Jul 24, 2025

• molecule-signature

  Public
  Signature based molecule enumeration from morgan fingerprints

  synthetic-biologyfingerprintchemoinformatics+ 1generative-ai

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 17, 2025Jun 17, 2025

• RetroPathRL

  Public
  Reinforcement Learning based bioretrosynthesis tool

  synthetic-biologysynbiometabolic-engineering+ 1retropath

  Python

  •

  MIT License

  •18•50•1•0•Updated Apr 2, 2025Apr 2, 2025

• RRParser

  Public
  Reaction rules parser

  Python

  •

  MIT License

  •0•2•0•0•Updated Mar 31, 2025Mar 31, 2025

• icfree-ml

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

  design-of-experimentslatin-hypercube-samplingcell-free+ 1machine-learning

  Python

  •

  MIT License

  •2•5•0•0•Updated Feb 20, 2025Feb 20, 2025

• PINN

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• icfree-feedstock

  Public
  A conda-smithy repository for icfree.

  BSD 3-Clause "New" or "Revised" License

  •4•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.6k•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• brs-utils

  Public
  Utilities

  Python

  •

  MIT License

  •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

• neo4jsbml

  Public
  Bridge the gap between SBML data and Neo4j

  bioinformaticsneo4jsbml

  Python

  •

  MIT License

  •0•4•0•1•Updated Sep 2, 2024Sep 2, 2024

• extractor_brendapy

  Public
  Python

  •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• amn_release

  Public
  Jupyter Notebook

  •

  MIT License

  •5•13•3•1•Updated May 8, 2024May 8, 2024

• straindesign

  Public
  Library to perform metabolic engineering tasks

  flux-balance-analysismetabolic-engineeringmetabolic-pathways+ 1bioinformatics

  Python

  •

  MIT License

  •0•5•2•1•Updated Apr 29, 2024Apr 29, 2024

• brendapy

  Public
  BRENDA parser in python

  Python

  •

  GNU Lesser General Public License v3.0

  •6•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• neo4jsbml-feedstock

  Public
  A conda-smithy repository for neo4jsbml.

  BSD 3-Clause "New" or "Revised" License

  •2•0•0•0•Updated Mar 4, 2024Mar 4, 2024

• galaxy

  Public
  Data intensive science for everyone.

  Python

  •

  Other

  •1.1k•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• tools-iuc

  Public
  Tool Shed repositories maintained by the Intergalactic Utilities Commission

  HTML

  •

  MIT License

  •474•0•0•0•Updated Feb 15, 2024Feb 15, 2024

• AMN_refactor

  Public
  This is a simple refactorization of some use case of the AMN code

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Feb 12, 2024Feb 12, 2024