SBML
SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.
Here are 140 public repositories matching this topic...
Antimony language support for IntelliJ Platform IDEs
-
Updated
Jun 10, 2024 - Java
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
-
Updated
Jun 10, 2024 - Python
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
-
Updated
Jun 11, 2024 - TypeScript
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.
-
Updated
Jun 8, 2024 - Python
Spatial bio-chemical reaction model editor and simulator
-
Updated
Jun 10, 2024 - C++
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
-
Updated
Jun 4, 2024 - Julia
A web application to visualize and edit pathway models
-
Updated
Jun 12, 2024 - JavaScript
CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]
-
Updated
May 30, 2024 - Python
Advanced Multilanguage Interface to CVODES and IDAS
-
Updated
Jun 12, 2024 - Jupyter Notebook
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.
-
Updated
May 26, 2024 - C++
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
-
Updated
Jun 12, 2024
Web application for converting from Heta into different modeling formats
-
Updated
May 20, 2024 - JavaScript
various libraries statically compiled for linux / macOS / windows
-
Updated
May 15, 2024 - Shell
CBMPy is a Python based platform for constraint based modelling and analysis.
-
Updated
May 12, 2024 - Python
The official PySCeS project source code repository.
-
Updated
May 13, 2024 - Python
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!
-
Updated
Jun 10, 2024 - Python