Repositories list

• SPECIMEN

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

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•5•14•0•Updated Dec 10, 2024Dec 10, 2024

• refinegems

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

  Jupyter Notebook

  •

  MIT License

  •1•10•20•0•Updated Dec 4, 2024Dec 4, 2024

• BOFdat

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

  Jupyter Notebook

  •

  Other

  •6•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• SBSCL

  Public
  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-programmingordinary-differential-equationsnumerical-simulationsode-solversteady-state+ 8

  HTML

  •

  GNU Lesser General Public License v3.0

  •13•21•15•0•Updated Dec 2, 2024Dec 2, 2024

• ModelPolisher

  Public
  ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

  systems-biologymodel-checkingknowledge-representation+ 3model-annotationsbmlbigg-models-knowledgebase

  Java

  •7•23•14•0•Updated Dec 1, 2024Dec 1, 2024

• MPClient

  Public
  Client library for the MPServer

  Python

  •0•2•0•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

• MassChargeCuration

  Public
  Python module to automatically curate the mass and charge assignments for metabolites in a metabolic model.

  Jupyter Notebook

  •1•4•0•0•Updated Oct 10, 2024Oct 10, 2024

• SBOannotator

  Public
  SBOannotator: A Python tool for the automated assignment of Systems Biology Onotology terms

  pythonautomationsoftware-development+ 5standardizationontologiessbocomputer-modelingmodel-repro

  Python

  •

  GNU General Public License v3.0

  •1•8•1•0•Updated Jul 15, 2024Jul 15, 2024

• EscherConverter

  Public
  A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

  flaskcommand-linesystems-biology+ 6computational-biologysbmljavaconvertsstandaloneescher

  Java

  •

  MIT License

  •10•15•11•0•Updated Jul 11, 2024Jul 11, 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
  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

  •

  GNU General Public License v3.0

  •5•12•1•0•Updated Mar 20, 2024Mar 20, 2024

• R-DRUGS

  Public
  Rationalized Discovery of Robust antiviral targets Using Genome-scale model Systems

  Jupyter Notebook

  •

  MIT License

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

• ModelEditingTools

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

  Java

  •

  MIT License

  •1•3•0•0•Updated Aug 29, 2023Aug 29, 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.

  visualizationkeggkegg-pathway+ 7conversiongmlgraphmlsbmlbiopaxkgml-fileskegg-pathway-database

  Java

  •

  GNU Lesser General Public License v3.0

  •12•18•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•0•1•0•Updated Jan 16, 2023Jan 16, 2023

• SBMLme

  Public
  Encoding ME models in SBML

  modelingsystems-biologygene-expression+ 4metabolismsbolsbmlencoding

  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

  •5•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.

  solversimulation-frameworkstochastic-simulation-algorithm+ 1java

  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

  •

  MIT License

  •2•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

  •

  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

  computational-biologyinformation-extractionmathematical-modelling+ 16sbmlregulatory-networkbiological-networksmetabolic-engineeringreactionplugequation+ 9

  HTML

  •

  GNU General Public License v3.0

  •0•4•6•0•Updated Mar 16, 2021Mar 16, 2021

• S_aureus_GEMs_Collection

  Public
  In this resporitory, all modifications made within the publication "Curating and comparing 114 Strain-Specific Genome-Scale Models of Staphylococcus aureus" are documented.

  Jupyter Notebook

  •2•4•2•0•Updated Jan 24, 2021Jan 24, 2021

• VisSim

  Public
  Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing based on SBSCL.

  systems-biologyordinary-differential-equationssbml-simulation+ 2sbmlinsilico

  Java

  •

  MIT License

  •1•2•0•0•Updated Jul 11, 2020Jul 11, 2020

• insilico

  Public
  InSilico

  frameworkplugin-managergraphical-user-interface

  Java

  •

  MIT License

  •2•7•6•1•Updated Jul 11, 2020Jul 11, 2020

• SBMLsimulator

  Public
  An efficient Java™ solver implementation for SBML

  systems-biologysimulation-frameworkcommand-line-tool+ 12parameter-estimationmodel-calibrationgraphical-user-interfaceode-solversbmlfbased-ml+ 5

  Java

  •

  GNU Lesser General Public License v3.0

  •1•4•2•0•Updated Jun 2, 2020Jun 2, 2020

• SysBio

  Public
  A convenient library that greatly simplifies application development with Java™

  bioinformaticsparser-librarysystems-biology+ 5application-launcherapplication-frameworkswing-guisbmlcommand-line-interface

  Java

  •

  Other

  •2•1•2•0•Updated Aug 28, 2019Aug 28, 2019