Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: sbml

Repositories

hetalang/heta-online

Web application for converting from Heta into different modeling formats

Language: JavaScript - Size: 86.3 MB - Last synced: about 4 hours ago - Pushed: about 6 hours ago - Stars: 0 - Forks: 0

AMICI-dev/AMICI

Advanced Multilanguage Interface to CVODES and IDAS

Language: Jupyter Notebook - Size: 209 MB - Last synced: about 9 hours ago - Pushed: about 11 hours ago - Stars: 106 - Forks: 30

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Language: Python - Size: 362 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 161 - Forks: 60

spatial-model-editor/spatial-model-editor

Spatial bio-chemical reaction model editor and simulator

Language: C++ - Size: 27.9 MB - Last synced: about 7 hours ago - Pushed: 1 day ago - Stars: 14 - Forks: 6

cthoyt/biomodels-metadata-analysis

Generate a summary of metadata annotations in the BioModels database

Language: Python - Size: 224 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

PySCeS/pysces

The official PySCeS project source code repository.

Language: Python - Size: 11 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 33 - Forks: 10

SystemsBioinformatics/cbmpy

CBMPy is a Python based platform for constraint based modelling and analysis.

Language: Python - Size: 35.1 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 16 - Forks: 6

Benchmarking-Initiative/Benchmark-Models-PEtab

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

Language: Python - Size: 2.88 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 23 - Forks: 14

biosimulators/Biosimulators_PySCeS

PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 1.75 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

sbmlteam/libsbml

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.

Language: C++ - Size: 259 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 36 - Forks: 27

copasi/copasi-dependencies

Collection of OpenSource libraries to simplify COPASI build

Language: C++ - Size: 88.7 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 7 - Forks: 3

opencobra/cobrapy

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

Language: Python - Size: 60.6 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 444 - Forks: 211

biosimulators/Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface

Language: Python - Size: 595 KB - Last synced: about 20 hours ago - Pushed: about 23 hours ago - Stars: 13 - Forks: 0

c-mayer/ECMproject

ECMproject is a standalone python program, which enumerates Elementary Conversion Modes (ECMs) of metabolic models.

Language: Jupyter Notebook - Size: 4.68 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

dweindl/sbmlmath

SBML MathML <-> SymPy

Language: Python - Size: 42 KB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 5 - Forks: 0

kmaeda16/RCGAToolbox

RCGAToolbox is a MATLAB toolbox for parameter estimation of kinetic models.

Language: MATLAB - Size: 57.1 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 3 - Forks: 1

matthiaskoenig/sbmlutils

Python utilities for SBML

Language: HTML - Size: 331 MB - Last synced: about 16 hours ago - Pushed: about 1 month ago - Stars: 36 - Forks: 12

biosimulations/biosimulations

A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

Language: TypeScript - Size: 193 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 37 - Forks: 13

sys-bio/roadrunner Fork of AndySomogyi/sbmlsolver

libRoadRunner: A high-performance SBML simulator

Language: C++ - Size: 272 MB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 36 - Forks: 25

matthiaskoenig/parameter-variability

Bayesian models for ODE models in the Systems Biology Markup Language (SBML)

Language: Python - Size: 2.48 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

biosimulators/Biosimulators_AMICI

AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.5 MB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 2 - Forks: 1

yaml2sbml-dev/yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.

Language: Python - Size: 1.4 MB - Last synced: 26 days ago - Pushed: 11 months ago - Stars: 12 - Forks: 6

fbergmann/pyodide-copasi

Vue3 Project using Pyodide / basico and python-copasi emscripten

Language: CSS - Size: 3.41 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 0 - Forks: 0

Fxe/kbase-SBMLTools

Language: Java - Size: 61.7 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 2 - Forks: 2

PEtab-dev/libpetab-python

Python package for working with PEtab files

Language: Python - Size: 10.6 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 14 - Forks: 5

spatial-model-editor/sme_deps_common

various libraries statically compiled for linux / macOS / windows

Language: Shell - Size: 345 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

SciML/SBMLToolkit.jl

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

Language: Julia - Size: 1.79 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 35 - Forks: 8

sbmlteam/jsbml

JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

Language: Java - Size: 301 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 35 - Forks: 24

sbmlteam/deviser

Design Explorer and Viewer for Iterative SBML Enhancement of Representations

Language: C++ - Size: 34.9 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 5 - Forks: 5

opencobra/memote

memote – the genome-scale metabolic model test suite

Language: HTML - Size: 12.1 MB - Last synced: about 7 hours ago - Pushed: 4 months ago - Stars: 122 - Forks: 26

carrascomj/rust_sbml

SBML parser + bindings to python

Language: Rust - Size: 163 KB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 6 - Forks: 3

opencobra/jeweler

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

Language: Nextflow - Size: 2.16 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

lobolab/mergem

mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models

Language: Python - Size: 9.62 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 7 - Forks: 0

brsynth/neo4jsbml

Bridge the gap between SBML data and Neo4j

Language: Python - Size: 27.8 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 4 - Forks: 0

PEtab-dev/PEtab

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

Size: 10.4 MB - Last synced: about 6 hours ago - Pushed: about 7 hours ago - Stars: 54 - Forks: 12

sbmlteam/python-libsbml

Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.

Language: Python - Size: 14.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 21 - Forks: 6

cnapy-org/CNApy

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Language: Python - Size: 6.92 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 41 - Forks: 7

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: 2 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

funasoul/celldesigner-parser

Parse CellDesigner annotations from SBML.

Language: Java - Size: 11.1 MB - Last synced: 2 months ago - Pushed: almost 7 years ago - Stars: 4 - Forks: 2

iVis-at-Bilkent/newt

A web application to visualize and edit pathway models

Language: JavaScript - Size: 43 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 50 - Forks: 26

BuildACell/subsbml

Python package for managing systems and subsystems of SBML models

Language: Jupyter Notebook - Size: 2.27 MB - Last synced: 25 days ago - Pushed: over 3 years ago - Stars: 5 - Forks: 5

LCSB-BioCore/SBML.jl

Julia interface to the Systems Biology Markup Language (SBML) library

Language: Julia - Size: 1.49 MB - Last synced: 7 days ago - Pushed: 5 months ago - Stars: 28 - Forks: 12

maurosilber/biomodels

Python library to download and cache models from BioModels

Language: Python - Size: 30.3 KB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

flintproject/Flint

A simulator for biological and physiological models

Language: C++ - Size: 116 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 3

charlesrocabert/MetEvolSim

MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.

Language: Python - Size: 43 MB - Last synced: 14 days ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

ICB-DCM/parPE

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

Language: C++ - Size: 55.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 4

sbmlteam/sbml-test-suite

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

Language: JavaScript - Size: 389 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 22 - Forks: 12

EBI-BioModels/SBO

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

Size: 705 KB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

matthiaskoenig/sbmlsim

sbmlsim: SBML simulation made easy

Language: HTML - Size: 60.9 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 5 - Forks: 4

sbmlteam/sbml-org-website

The source code and issue tracker for the SBML.org website.

Language: HTML - Size: 400 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 8 - Forks: 4

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: 4 months ago - Pushed: 10 months ago - Stars: 20 - Forks: 12

draeger-lab/KEGGtranslator

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.

Language: Java - Size: 63.7 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 14 - Forks: 10

matthiaskoenig/dfba

Encoding Dynamic Flux Balance Analysis in SBML

Language: HTML - Size: 85.6 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 11 - Forks: 1

matthiaskoenig/cy3sbml

cy3sbml: SBML for Cytoscape 3

Language: Java - Size: 326 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 11 - Forks: 2

LoLab-MSM/pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

Language: Jupyter Notebook - Size: 23.5 MB - Last synced: 21 days ago - Pushed: about 1 year ago - Stars: 27 - Forks: 4

draeger-lab/SBML2LaTeX

SBML2LATEX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate report from SBML in form of PDF or TeX, which can be further processed to various file types including DVI, PS, EPS, GIF, JPG, or PNG. SBML2LATEX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LATEX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication.

Language: TeX - Size: 180 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 5 - Forks: 3

matthiaskoenig/fbc_curation

FROG analysis in python for the reproducibility of FBC models

Language: Python - Size: 19 MB - Last synced: 13 days ago - Pushed: about 1 year ago - Stars: 8 - Forks: 3

darrenjw/smfsb

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

Language: AMPL - Size: 60.5 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 29 - Forks: 6

sys-bio/simplesbml

Python package for building SBML models without needing to use libSBML.

Language: Python - Size: 6.1 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 11 - Forks: 12

sys-bio/libSBMLVisual

libSBNW is a network viewer which supports autolayout of reaction networks and uses libSBML for reading/writing models.

Language: C++ - Size: 370 KB - Last synced: 9 months ago - Pushed: about 6 years ago - Stars: 3 - Forks: 1

sbgn/cd2sbgnml Fork of royludo/cd2sbgnml

Translation between CellDesigner-flavoured SBML and SBGN-ML

Language: Java - Size: 21.1 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 6 - Forks: 2

Romain-P/SBMLparser

epitech sbml parser & json converter project | 100%

Language: C - Size: 2.39 MB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 3 - 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: 25 days ago - Pushed: about 2 years ago - Stars: 5 - Forks: 1

biosimulators/Biosimulators_tellurium

tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 2.62 MB - Last synced: 30 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 2

soli/casq

CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]

Language: Python - Size: 585 KB - Last synced: 4 days ago - Pushed: 2 months ago - Stars: 2 - Forks: 2

nicolas-gi/SBMLparser

Parser for SBML files, synthesis pool project.

Language: C - Size: 11.7 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

matthiaskoenig/iri-model

Hepatocyte model of ischemia reperfusion injury (IRI)

Size: 38.1 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

libsbmlsim/libsbmlsim

LibSBMLSim: A library for simulating SBML models

Language: C - Size: 33.6 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 13 - Forks: 7

gibbslab/minval

An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

Language: R - Size: 7.1 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1

draeger-lab/SBMLme

Encoding ME models in SBML

Language: Java - Size: 17.9 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 7 - Forks: 2

draeger-lab/ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

Language: Java - Size: 60.5 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 6

biosimulations/biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

Language: Python - Size: 259 MB - Last synced: 24 days ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

biosimulators/Biosimulators_test_suite

Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators

Language: Python - Size: 54.3 MB - Last synced: 30 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 2

biosimulators/Biosimulators_COPASI

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Language: Python - Size: 8.23 MB - Last synced: about 20 hours ago - Pushed: 2 months ago - Stars: 2 - Forks: 3

NSR-Physiome/JSim

JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains.

Language: Java - Size: 206 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 4