Python utilities for SBML
☆41Aug 6, 2026Updated 3 weeks ago
Alternatives and similar repositories for sbmlutils
Users that are interested in sbmlutils are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Encoding Dynamic Flux Balance Analysis in SBML☆13Sep 16, 2020Updated 5 years ago
- cy3sbml: SBML for Cytoscape 3☆15Jan 22, 2026Updated 7 months ago
- MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.☆13Aug 21, 2024Updated 2 years ago
- LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (…☆55Updated this week
- Python library for SBGN☆11May 19, 2026Updated 3 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Ontology of algorithms for analyzing biological models, their parameters, and their outputs☆12Mar 31, 2026Updated 5 months ago
- libRoadRunner: A high-performance SBML simulator☆62Updated this week
- Libraries for the Systems Biology Graphical Notation (SBGN); Java and C++☆21Oct 8, 2024Updated last year
- Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.☆24Mar 9, 2026Updated 5 months ago
- PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology☆64Jun 22, 2026Updated 2 months ago
- Import SBML dynamic models into the Julia SciML ecosystem for jump (Gillespie), SDE, and ODE simulations☆24Updated this week
- Julia for Systems Biology Workshop @JuliaCon 2024☆13Jul 8, 2024Updated 2 years ago
- Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.☆21Jul 14, 2026Updated last month
- A collection of M models downloaded from published studies☆18Feb 18, 2016Updated 10 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Metabolic In silico Network Expansion (MINE) Database Construction and DB Logic☆22Apr 21, 2026Updated 4 months ago
- A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existin…☆35Jul 21, 2026Updated last month
- A simplified python interface to COPASI.☆28Jun 15, 2026Updated 2 months ago
- Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices☆26Updated this week
- Tool to convert an ODE model specified in the YAML format to SBML.☆13Jun 13, 2023Updated 3 years ago
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆28Mar 13, 2023Updated 3 years ago
- Python solution for the application of machine learning to Pop PK model selection.☆32Jul 27, 2026Updated last month
- A COBRApy extension for genome-scale models of metabolism and expression (ME-models)☆40Jan 11, 2019Updated 7 years ago
- A Universal Modeling Language for Metabolic Flux Analysis☆12Aug 10, 2026Updated 3 weeks ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data☆28Jul 6, 2023Updated 3 years ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆20May 26, 2026Updated 3 months ago
- 📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology☆33Dec 16, 2019Updated 6 years ago
- ☆22Updated this week
- A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results☆44Updated this week
- The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in part…☆12May 16, 2023Updated 3 years ago
- Open source genome-scale metabolic models of human and model animals☆27May 5, 2026Updated 3 months ago
- The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML suppor…☆27Dec 3, 2025Updated 8 months ago
- The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the …☆26Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…☆25Updated this week
- Dugong - Scientific Linux Container☆17Jul 25, 2018Updated 8 years ago
- Python package for building SBML models without needing to use libSBML.☆11Aug 18, 2021Updated 5 years ago
- Trust Region Optimization in Python☆28Nov 11, 2025Updated 9 months ago
- Rule-based modeling framework☆70Aug 12, 2026Updated 2 weeks ago
- A web application to visualize and edit pathway models☆62Updated this week
- Create and fit parameter-estimation problems for ODE and SciML models in Julia, leveraging the Julia SciML ecosystem.☆71Updated this week