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The Top 23 Sbml Open Source Projects

Open source projects categorized as Sbml
Categories > Sbml
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101most recent commit 8 months agopypi cobra} Downloads
Indra ⭐ 154
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.
dependent packages 7total releases 29most recent commit 5 months agopypi indra} Downloads
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61most recent commit 6 months agopypi memote} Downloads
Amici ⭐ 105
Advanced Multilanguage Interface to CVODES and IDAS
dependent packages 7total releases 105most recent commit 2 months agopypi amici} Downloads
Petab ⭐ 54
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
most recent commit 3 months ago
Newt ⭐ 48
A web application to visualize and edit pathway models
most recent commit a year ago
Biosimulations ⭐ 36
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
most recent commit 5 months ago
Cnapy ⭐ 36
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!
most recent commit 5 months ago
Sbmltoolkit.jl ⭐ 35
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
most recent commit 5 months ago
Jsbml ⭐ 34
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.
dependent packages 7total releases 9most recent commit a year ago
Sbmlutils ⭐ 31
Python utilities for SBML
dependent packages 2total releases 59most recent commit 9 months agopypi sbmlutils} Downloads
Libsbml ⭐ 31
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.
most recent commit 7 months ago
Smfsb ⭐ 29
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
most recent commit 6 months ago
Pysces ⭐ 29
The official PySCeS project source code repository.
most recent commit 6 months ago
Sbml.jl ⭐ 27
Julia interface to the Systems Biology Markup Language (SBML) library
most recent commit 6 months ago
Pyvipr ⭐ 25
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
most recent commit 2 years ago
Roadrunner ⭐ 25
libRoadRunner: A high-performance SBML simulator
most recent commit 3 years ago
Benchmark Models Petab ⭐ 23
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
total releases 1most recent commit 6 months ago
Modelpolisher ⭐ 23
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
most recent commit 2 years ago
Sbml Test Suite ⭐ 21
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.
most recent commit 2 years ago
Parpe ⭐ 19
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
most recent commit 6 months ago
Python Libsbml ⭐ 19
Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.
most recent commit 8 months ago
Sbscl ⭐ 19
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.
most recent commit a year ago
The 10 Most Depended On Sbml Open Source Projects
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101latest release October 31, 2023most recent commit 8 months agopypi cobra} Downloads
Amici ⭐ 105
Advanced Multilanguage Interface to CVODES and IDAS
dependent packages 7total releases 105latest release November 21, 2023most recent commit 2 months agopypi amici} Downloads
Simplesbml ⭐ 8
Python package for building SBML models without needing to use libSBML.
dependent packages 4total releases 20latest release August 18, 2021most recent commit 3 years agopypi simplesbml} Downloads
Cbmpy ⭐ 13
CBMPy is a Python based platform for constraint based modelling and analysis.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 8 months agopypi cbmpy} Downloads
Sbmlutils ⭐ 31
Python utilities for SBML
dependent packages 2total releases 59latest release September 28, 2023most recent commit 9 months agopypi sbmlutils} Downloads
Yaml2sbml ⭐ 13
Tool to convert an ODE model specified in the YAML format to SBML.
dependent packages 1total releases 6latest release July 30, 2021most recent commit 2 years agopypi yaml2sbml} Downloads
Rust_sbml ⭐ 6
SBML parser + bindings to python
dependent packages 1total releases 16latest release November 01, 2021most recent commit 2 years agocargo rust_sbml} Downloads
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61latest release November 21, 2023most recent commit 6 months agopypi memote} Downloads
The 10 Latest Releases In Sbml Open Source Projects
Amici ⭐ 105
Advanced Multilanguage Interface to CVODES and IDAS
dependent packages 7total releases 105latest release November 21, 2023most recent commit 2 months agopypi amici} Downloads
Memote ⭐ 117
memote – the genome-scale metabolic model test suite
dependent packages 1total releases 61latest release November 21, 2023most recent commit 6 months agopypi memote} Downloads
Cbmpy ⭐ 13
CBMPy is a Python based platform for constraint based modelling and analysis.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 8 months agopypi cbmpy} Downloads
Cobrapy ⭐ 414
COBRApy is a package for constraint-based modeling of metabolic networks.
dependent packages 84total releases 101latest release October 31, 2023most recent commit 8 months agopypi cobra} Downloads
Sbmlutils ⭐ 31
Python utilities for SBML
dependent packages 2total releases 59latest release September 28, 2023most recent commit 9 months agopypi sbmlutils} Downloads
Fbc_curation ⭐ 7
FROG analysis in python for the reproducibility of FBC models
total releases 12latest release May 19, 2022most recent commit a year ago
Rust_sbml ⭐ 6
SBML parser + bindings to python
dependent packages 1total releases 16latest release November 01, 2021most recent commit 2 years agocargo rust_sbml} Downloads
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