draeger-lab/SBSCL

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.

Language: HTML - Size: 237 MB - Last synced at: 1 day ago - Pushed at: 11 days ago - Stars: 25 - Forks: 18

opencobra/cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

Language: Python - Size: 60 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 513 - Forks: 227

PEtab-dev/PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

Size: 11.5 MB - Last synced at: 3 days ago - Pushed at: 13 days ago - Stars: 60 - Forks: 12

klamt-lab/COBRA-k

A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation:

Language: Python - Size: 201 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 1

spatial-model-editor/spatial-model-editor

Spatial bio-chemical reaction model editor and simulator

Language: C++ - Size: 40 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 18 - Forks: 8

opencobra/jeweler

Test and grade genome-scale metabolic models (GEMs).

Language: Nextflow - Size: 2.16 MB - Last synced at: 3 days ago - Pushed at: 25 days ago - Stars: 1 - Forks: 0

BeeAnka/EFMlrs

Python package and workflow for EFM calculation via (mp)lrs and efmtool

Language: Python - Size: 5.37 MB - Last synced at: 6 days ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 1

matthiaskoenig/glimepiride-app

Glimepiride Web Application

Language: Python - Size: 4.19 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

matthiaskoenig/canagliflozin-model

Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin

Language: HTML - Size: 23.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

hydraharish123/NetworkAnalyzer

Language: JavaScript - Size: 261 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

matthiaskoenig/tirzepatide-model

Physiologically based pharmacokinetics (PBPK) model of tirzapetide

Language: HTML - Size: 14 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

draeger-lab/pymCADRE

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

Language: Jupyter Notebook - Size: 37.5 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 6

paulflang/SbmlInterface.jl

Interface between the Systems Biology Markup Language and Julia

Language: Julia - Size: 303 KB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 2

r-costa/sbml2hyb

sbml2hyb is a tool for SBML compatible hybrid modelling of biological systems

Language: Python - Size: 31.7 MB - Last synced at: 21 days ago - Pushed at: 11 months ago - Stars: 5 - Forks: 2

draeger-lab/C_striatum_GEMs

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

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ayush9pandey/subsbml Fork of BuildACell/subsbml

Python package for managing systems and subsystems of SBML models

Language: Jupyter Notebook - Size: 3.82 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 1

bo-dun/IBW_SBML_SBOL_Export

Final Infobiotics Workbench implementation of SBOL and SBML conversion functionality, UI updates, and sequence fetching

Language: Java - Size: 67.4 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1

paulflang/SBML2Julia

A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.

Language: Python - Size: 20.5 MB - Last synced at: 8 days ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 1

matthiaskoenig/iri-model

Hepatocyte model of ischemia reperfusion injury (IRI)

Size: 38.1 KB - Last synced at: 7 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

opencobra/memote-docker

Easily use the memote command line interface from a docker container.

Language: Shell - Size: 170 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 2

draeger-lab/BioModelsEd

A graphical editor for systems biology models.

Language: Java - Size: 4.8 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1