Repositories list

• BioBot

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 17, 2026Apr 17, 2026

• galaxytools

  Public
  Galaxy wrappers of SynBioCAD tools suite

  synthetic-biologysystems-biologygalaxy-project

  synthetic-biologysystems-biologygalaxy-project

  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•33 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rpThermo

  Public
  Thermodynamics of metabolic pathways

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• rpCompletion

  Public
  Mono-component reactions completion

  Python

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• rpExtractSink

  Public
  RetroPath2 sink generator

  Python

  •00 forks•11 star•11 issue•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• rplibs

  Public
  Libraries for rpTools

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• rpFBA

  Public
  Perform Flux Balance Analysis on a single or collection of SBML files containing heterologous pathways.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• amn_library

  Public
  AMN conda package

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• rr_cache

  Public
  RetroRules Cache

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• rxn_rebuild

  Public
  Rebuild full reaction from reaction rule

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• brs-utils

  Public
  Utilities

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• chemproflow

  Public
  Assessing substrate transport across cell membranes

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 8, 2026Mar 8, 2026

• damn_library

  Public
  damn conda package

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• rptools

  Public
  Suite of tools that work on rpSBML format

  synthetic-biologysystems-biologysynbio+ 1

  synthetic-biologysystems-biologysynbiometabolic-engineering

  HTML

  •

  MIT License

  •22 forks•77 stars•66 issues•22 pull requests•Updated Feb 20, 2026Feb 20, 2026

• retropath2-wrapper

  Public
  Python wrapper for Retropath2.0 Knime workflow

  synthetic-biologysynbiometabolic-engineering

  synthetic-biologysynbiometabolic-engineering

  JavaScript

  •

  MIT License

  •11 fork•99 stars•00 issues•00 pull requests•Updated Feb 12, 2026Feb 12, 2026

• mutant-covid

  Public
  statistics for ecoli mutants on covid patients classification

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• amn_light

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 3, 2026Feb 3, 2026

• rp2paths

  Public
  RetroPath2.0 to pathways

  synthetic-biologysynbio

  synthetic-biologysynbio

  Python

  •

  MIT License

  •1010 forks•1818 stars•00 issues•00 pull requests•Updated Jan 28, 2026Jan 28, 2026

• Simulated-based-inference

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 27, 2026Jan 27, 2026

• active_learning_cobra

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 27, 2026Jan 27, 2026

• al_cluster_margin

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 26, 2026Jan 26, 2026

• bacterial_rc

  Public
  Living bacterial reservoir computers for information processing and sensing

  synthetic-biologyreservoir-computing

  synthetic-biologyreservoir-computing

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• molecule-signature

  Public
  Signature based molecule enumeration from morgan fingerprints

  synthetic-biologyfingerprintchemoinformatics+ 1

  synthetic-biologyfingerprintchemoinformaticsgenerative-ai

  Python

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• dAMN-main-release

  Public
  This repository contains the reference implementation of dAMN, a hybrid modelling framework that combines: - a neural network predicting effective intracellular…

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 12, 2025Dec 12, 2025

• molecule-signature-paper

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

  chemistrysignaturefingerprint+ 4

  chemistrysignaturefingerprintgenerative-modelchemoinformaticsmolecular-generationdeterministic-enumeration

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•11 pull request•Updated Nov 24, 2025Nov 24, 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 differenti…

  Jupyter Notebook

  •22 forks•00 stars•00 issues•00 pull requests•Updated Oct 7, 2025Oct 7, 2025

• Bayesian-Experimental-Design-BED-

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 30, 2025Sep 30, 2025

• reservoir

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 19, 2025Sep 19, 2025

• active_learning_cell_free

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

  Jupyter Notebook

  •1212 forks•1313 stars•00 issues•00 pull requests•Updated Sep 17, 2025Sep 17, 2025

• biorgroup

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

  r-groupchebirhea

  r-groupchebirhea

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 3, 2025Sep 3, 2025