sbml

There are 141 repositories under sbml topic.

  • opencobra/cobrapy

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

    Language:Python45338660211

  • sorgerlab/indra

    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:Python1652346062

  • opencobra/memote

    memote – the genome-scale metabolic model test suite

    Language:HTML1232046826
  • AMICI

    AMICI-dev/AMICI

    Advanced Multilanguage Interface to CVODES and IDAS

    Language:Jupyter Notebook1071293230
  • PEtab

    PEtab-dev/PEtab

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

    551622912

  • iVis-at-Bilkent/newt

    A web application to visualize and edit pathway models

    Language:JavaScript511267127
  • CNApy

    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:Python4232227
  • libsbml

    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++381015528

  • 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:Java372617524

  • SciML/SBMLToolkit.jl

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

    Language:Julia379198
  • biosimulations

    biosimulations/biosimulations

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

    Language:TypeScript3671.3k13

  • matthiaskoenig/sbmlutils

    Python utilities for SBML

    Language:HTML36633112

  • sys-bio/roadrunner

    libRoadRunner: A high-performance SBML simulator

    Language:C++361774124

  • PySCeS/pysces

    The official PySCeS project source code repository.

    Language:Python3446510

  • darrenjw/smfsb

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

    Language:AMPL31435

  • LCSB-BioCore/SBML.jl

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

    Language:Julia2896912

  • LoLab-MSM/pyvipr

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

    Language:Jupyter Notebook277264

  • 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:Python241410514

  • 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:JavaScript2387012

  • draeger-lab/ModelPolisher

    ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

    Language:Java2215836

  • sbmlteam/python-libsbml

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

    Language:Python217296

  • 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:HTML2095413
  • parPE

    ICB-DCM/parPE

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

    Language:C++1972004

  • 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:Java1761012

  • SystemsBioinformatics/cbmpy

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

    Language:Python174265

  • draeger-lab/EscherConverter

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

    Language:Java1573410

  • PEtab-dev/libpetab-python

    Python package for working with PEtab files

    Language:Python149785
  • spatial-model-editor

    spatial-model-editor/spatial-model-editor

    Spatial bio-chemical reaction model editor and simulator

    Language:C++1424786
  • Biosimulators

    biosimulators/Biosimulators

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

    Language:Python13115510

  • matthiaskoenig/cy3sbml

    cy3sbml: SBML for Cytoscape 3

    Language:Java1353062

  • libsbmlsim/libsbmlsim

    LibSBMLSim: A library for simulating SBML models

    Language:C123137

  • yaml2sbml-dev/yaml2sbml

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

    Language:Python124666

  • matthiaskoenig/dfba

    Encoding Dynamic Flux Balance Analysis in SBML

    Language:HTML116161

  • sys-bio/simplesbml

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

    Language:Python11142712

  • 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.

    9382

  • sbmlteam/sbml-org-website

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

    Language:HTML97404