Repositories list

• refinegems

  Public
  refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).

  Python

  •

  MIT License

  •2•16•22•0•Updated Dec 17, 2025Dec 17, 2025

• OptSolvX

  Public
  Provides a unified and flexible Java interface for mathematical optimization using multiple solver backends.

  Java

  •

  MIT License

  •0•2•1•2•Updated Dec 14, 2025Dec 14, 2025

• SPECIMEN

  Public
  Automated pipeline for strain-specific metabolic modeling based on a high-quality template model.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•5•20•1•Updated Dec 2, 2025Dec 2, 2025

• SBSCL

  Public

  draeger-lab/SBSCL’s past year of commit activity
  The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

  javaapilibrary+ 15simulationsolverlinear-programmingsimulationsordinary-differential-equationsnumerical-simulationsode-solver+ 8

  HTML

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  GNU Lesser General Public License v3.0

  •19•25•20•7•Updated Oct 24, 2025Oct 24, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.7k•0•0•0•Updated Oct 9, 2025Oct 9, 2025

• GEM_Tutorial

  Public
  This repository contains the data, Jupyter Notebooks and setup for a workshop on the toolbox ``refineGEMs`` and the workflow collection ``SPECIMEN``.

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Sep 22, 2025Sep 22, 2025

• MassChargeCuration

  Public

  draeger-lab/MassChargeCuration’s past year of commit activity
  Python module to automatically curate the mass and charge assignments for metabolites in a metabolic model.

  Jupyter Notebook

  •3•5•3•1•Updated Sep 15, 2025Sep 15, 2025

• SBOannotator

  Public

  draeger-lab/SBOannotator’s past year of commit activity
  SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms

  pythonautomationsoftware-development+ 5standardizationontologiessbocomputer-modelingmodel-repro

  Python

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  GNU General Public License v3.0

  •4•8•1•3•Updated Jul 28, 2025Jul 28, 2025

• EscherConverter

  Public

  draeger-lab/EscherConverter’s past year of commit activity
  A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

  javaconvertsflask+ 6command-linesystems-biologystandalonecomputational-biologyeschersbml

  Java

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  MIT License

  •10•16•12•0•Updated Jul 9, 2025Jul 9, 2025

• .github

  Public

  draeger-lab/.github’s past year of commit activity
  0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

• R-DRUGS

  Public

  draeger-lab/R-DRUGS’s past year of commit activity
  Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems

  systems-biologydrug-discoverydrug-repurposing+ 3metabolic-modelsvirus-infectionantiviral-treatment

  Jupyter Notebook

  •

  MIT License

  •0•3•0•0•Updated Mar 28, 2025Mar 28, 2025

• ModelEditingTools

  Public
  A collection of tools for working with models in SBML format

  Java

  •

  MIT License

  •1•4•0•0•Updated Mar 28, 2025Mar 28, 2025

• ModelPolisher

  Public

  draeger-lab/ModelPolisher’s past year of commit activity
  ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

  systems-biologymodel-checkingknowledge-representation+ 3sbmlbigg-models-knowledgebasemodel-annotation

  Java

  •8•23•15•0•Updated Jan 28, 2025Jan 28, 2025

• TFpredict

  Public
  Identification and structural characterization of transcription factors based on supervised machine learning

  machine-learningbioinformaticstranscription-factors+ 7predictionidentificationfastablasttranscription-factorhomologysabine

  Java

  •

  GNU General Public License v3.0

  •3•7•1•0•Updated Jan 24, 2025Jan 24, 2025

• BOFdat

  Public
  Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

  Jupyter Notebook

  •

  Other

  •8•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• MPClient

  Public
  Client library for the MPServer

  Python

  •0•2•1•0•Updated Nov 29, 2024Nov 29, 2024

• MPServer

  Public
  Server Implementation for the Model Polisher

  Clojure

  •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

• C_striatum_GEMs

  Public
  This repository contains all changes made to the strain specific models of Corynebacterium striatum.

  pythonpathogenflux-balance-analysis+ 3constraint-based-modelingsbml-modelgenome-scale-metabolic-model

  HTML

  •

  MIT License

  •0•1•0•0•Updated May 22, 2024May 22, 2024

• pymCADRE

  Public

  draeger-lab/pymCADRE’s past year of commit activity
  pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

  pythonflux-balance-analysisconstraint-based-modeling+ 6sbml-modelsystems-biology-simulationgenome-scale-modelingtissue-specific-modelshost-virus-modelmetabolic-network-reconstruction

  Jupyter Notebook

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  GNU General Public License v3.0

  •7•14•2•0•Updated Mar 20, 2024Mar 20, 2024

• C_striatum_wetlab

  Public
  This repository contains data generated in the wet lab need for characterization and validation of strain specific GEMs

  Jupyter Notebook

  •0•1•0•0•Updated Nov 2, 2023Nov 2, 2023

• KEGGtranslator

  Public
  A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.

  visualizationconversiongml+ 7keggkegg-pathwaygraphmlsbmlbiopaxkgml-fileskegg-pathway-database

  Java

  •

  GNU Lesser General Public License v3.0

  •11•20•7•0•Updated Jun 26, 2023Jun 26, 2023

• SBSCL-demo

  Public
  A demo repository with example code for using the Systems Biology Simulation Core Library (SBSCL).

  javasimulationsystems-biology+ 3ordinary-differential-equationsstochastic-differential-equationsflux-balance-analysis

  Java

  •

  MIT License

  •0•1•1•0•Updated Jan 16, 2023Jan 16, 2023

• SBMLme

  Public
  Encoding ME models in SBML

  encodingmodelingsystems-biology+ 4gene-expressionmetabolismsbolsbml

  Java

  •

  MIT License

  •2•7•0•0•Updated Dec 21, 2022Dec 21, 2022

• pymCADRE-1

  Public
  pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •7•0•0•0•Updated Nov 11, 2022Nov 11, 2022

• SABINE

  Public
  Prediction of the binding specificity of transcription factors using support vector regression

  transcription-factor-bindingsequence-predictionprotein-dna-interactions+ 1bioinformatics-tool

  Java

  •

  GNU General Public License v3.0

  •2•3•2•0•Updated Feb 14, 2022Feb 14, 2022

• FERN

  Public
  FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java.

  javasolversimulation-framework+ 1stochastic-simulation-algorithm

  Java

  •

  GNU Lesser General Public License v3.0

  •3•1•1•0•Updated Feb 8, 2022Feb 8, 2022

• SBTabEditor

  Public
  Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

  editormodelingsystems-biology+ 3sbmltabular-interfacesbtab

  Java

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  MIT License

  •1•9•6•0•Updated Jan 11, 2022Jan 11, 2022

• Table2Model

  Public
  A parser for systems biology models published in a table form that produces standardized files, such as SBML.

  Java

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  MIT License

  •0•0•0•0•Updated Dec 9, 2021Dec 9, 2021

• SBVC

  Public
  Systems Biology Visualizer and Converter

  Java

  •

  GNU Lesser General Public License v3.0

  •1•1•0•0•Updated Sep 14, 2021Sep 14, 2021

• SBMLsqueezer

  Public
  Context-sensitive creation of kinetic equations in biochemical networks

  reactionplugequation+ 16systems-biologycomputational-biologyinformation-extractionreactionsmathematical-modellingsbmlregulatory-network+ 9

  HTML

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  GNU General Public License v3.0

  •0•5•7•0•Updated Mar 16, 2021Mar 16, 2021