Projects in Awesome Lists by brsynth
A curated list of projects in awesome lists by brsynth .
https://github.com/brsynth/active_learning_cell_free
Scripts to perform active learning as described in the referenced article.
Last synced: 16 Jan 2026
https://github.com/brsynth/retropath2-wrapper
Python wrapper for Retropath2.0 Knime workflow
metabolic-engineering synbio synthetic-biology
Last synced: 11 Apr 2026
https://github.com/brsynth/rptools
Suite of tools that work on rpSBML format
metabolic-engineering synbio synthetic-biology systems-biology
Last synced: 05 Jan 2026
https://github.com/brsynth/rpreactor
A command-line and python package to handle biochemical reaction rules.
biochemical-reactions reaction-rules retrorules
Last synced: 16 Jan 2026
https://github.com/brsynth/icfree-ml
Design of experiments (DoE) and machine learning packages for the iCFree project
cell-free design-of-experiments latin-hypercube-sampling machine-learning
Last synced: 16 Jan 2026
https://github.com/brsynth/straindesign
Library to perform metabolic engineering tasks
bioinformatics flux-balance-analysis metabolic-engineering metabolic-pathways
Last synced: 16 Jan 2026
https://github.com/brsynth/detectable_metabolites
Collection of compounds known for being detectable by a living cell, through the action of a genetically encoded biosensor
Last synced: 16 Jan 2026
https://github.com/brsynth/neo4jsbml
Bridge the gap between SBML data and Neo4j
Last synced: 16 Jan 2026
https://github.com/brsynth/metabolic_perceptrons
This repository contains the R scripts that generated the models for the Metabolic Perceptrons for Neural Computing in Biological Systems article present on bioarchive at https://doi.org/10.1101/616599
Last synced: 16 Jan 2026
https://github.com/brsynth/rxn_rebuild
Rebuild full reaction from reaction rule
Last synced: 10 Apr 2026
https://github.com/brsynth/rpchemtools
Minimalist toolbox to deal with chemicals
Last synced: 16 Jan 2026
https://github.com/brsynth/dnaweaver_synbiocad
Command-Line version of DNAWeaver
Last synced: 16 Jan 2026
https://github.com/brsynth/scope-viewer
Scope Viewer, a simple viewer for RetroPath suite results
Last synced: 16 Jan 2026
https://github.com/brsynth/damn
New hybrid machine learning model combining artificial neural network and a dynamic flux balance analysis on a metabolic model to predict bacterial growth curve.
Last synced: 16 Jan 2026
https://github.com/brsynth/ot-reproductibility
Testing Opentrons reproductibility
Last synced: 16 Jan 2026
https://github.com/brsynth/molecule-signature
Signature based molecule enumeration from morgan fingerprints
chemoinformatics fingerprint generative-ai synthetic-biology
Last synced: 16 Jan 2026
https://github.com/brsynth/plug_and_play_cell_free_model
This repository contains the R script that generated the model for the Plug-and-Play Metabolic Adapters Expand the Chemical Detection Space of Cell-Free Biosensors article. Full publication is available at https://www.nature.com/articles/s41467-019-09722-9 or https://doi.org/10.1038/s41467-019-09722-9.
Last synced: 16 Jan 2026
https://github.com/brsynth/taxonid
Get taxon id from NCBI taxonomy database
Last synced: 16 Jan 2026
https://github.com/brsynth/galaxytools
Galaxy wrappers of SynBioCAD tools suite
galaxy-project synthetic-biology systems-biology
Last synced: 16 Jan 2026
https://github.com/brsynth/biorgroup
Systematic expansion of R-group for ChEBI molecules from the RHEA database
Last synced: 16 Jan 2026
https://github.com/brsynth/pysbol
Extraction of SynBioDex / pySBOL for version 1 of pySBOL
Last synced: 16 Jan 2026
https://github.com/brsynth/amn_refactor
This is a simple refactorization of some use case of the AMN code
Last synced: 16 Jan 2026
https://github.com/brsynth/pinn-v2
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.
Last synced: 20 Jan 2026
https://github.com/brsynth/rpbasicdesign
Convert rpSBML file to SBOL + CSV files ready to be used by DNA-Bot.
dna-bot synbio synthetic-biology
Last synced: 21 Feb 2026
https://github.com/brsynth/molecule-signature-paper
Code supporting the paper 'Getting Molecules from their Fingerprints: Generative Models vs. Deterministic Enumeration'
chemistry chemoinformatics deterministic-enumeration fingerprint generative-model molecular-generation signature
Last synced: 16 Jan 2026
https://github.com/brsynth/rp2biosensor
Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output
Last synced: 18 Feb 2026
https://github.com/brsynth/rpfba
Perform Flux Balance Analysis on a single or collection of SBML files containing heterologous pathways.
Last synced: 02 May 2026
https://github.com/brsynth/pysbol2-conda-recipe
Instructions for building conda recipe for pySBOL2.
Last synced: 16 Jan 2026