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Softwares

  tellurium and     libRoadRunner

Tellurium is a self-contained Python-based environment for model building, simulation, and analysis that facilitates the reproducibility of models in systems and synthetic biology. Here are some of the features of Tellurium:

• A modular, cross-platform, and open-source simulation environment
• First-class support for standards in systems and synthetic biology (SBML, SED-ML, COMBINE, SBOL, etc.)
• Natively integrates libRoadRunner
• Supports Antimony, a human-readable model definition language which can be converted to and from SBML
• A fully configured Python distribution with standalone installation support

Download Tellurium now or run pip install tellurium

1. K. Choi, J.K. Medley, M. König, K. Stocking, L. Smith, S. Gu, H.M. Sauro. 2018. “Tellurium: An Extensible Python-based Modeling Environment for Systems and Synthetic Biology.” BioSystems. 171, 74–79. 10.1016/j.biosystems.2018.07.006.

2. J.K. Medley, K. Choi, M. König, L. Smith, S. Gu, J. Hellerstein, S.C. Sealfon, H.M. Sauro. 2018. “Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse.” PLOS Comp. Biol. 14 (6), e1006220. 10.1371/journal.pcbi.1006220.

Tellurium uses libRoadRunner, one of the fastest and most scalable SBML simulation engines for dynamical systems of reaction networks. Here are some of the features of libRoadRunner:

• A state-of-the-art high-performance and portable simulation engine for systems and synthetic biology
• Supports the latest SBML specification (except algebraic rules and delay package)
• LLVM JIT compiler leads to incredibly fast simulation speed
• Supports deterministic simulations (CVODE, Euler, RK45, etc.), stochastic simulations, steady-state analyses using NLEQ2 and others, metabolic control analysis, and many more.
• Supports plugin system for bifurcation analysis, parameter estimation, bootstrapping, etc.
• Native low-level parallelization support
• Pickled (serialized) RoadRunner
• On-the-run model editing
• Julia bindings

Download libRoadRunner now or run pip install libroadrunner

1. C. Welsh, J. Xu, L. Smith, M. König, K. Choi, H.M. Sauro. 2023. “libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library.” Bioinformatics. 39 (1), btac770. 10.1093/bioinformatics/btac770.

evoMEG

Evolutionary Algorithm-based Model Ensemble Generation Algorithm (evoMEG) is a powerful meta-modeling algorithm for biochemical reaction network models that generates a model ensemble from perturbation studies.

Check out evoMEG

  phraSED-ML

phraSED-ML is a human-readable simulation setup definition language which can be converted to and from SED-ML.

Download phraSED-ML now or run pip install phrasedml

1. K. Choi, L. Smith, J.K. Medley, H.M. Sauro. 2016. “phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.” J. Bioinform. Comput. Biol. 14 (6), 1650035. 10.1142/S0219720016500359.

netplotlib

netplotlib is a purely Python-based visual analysis tool for biochemical reaction network diagrams, utilizing NetworkX and matplotlib packages.

Download netplotlib now or run pip install netplotlib