ArticleBio Systems2018
Tellurium: An extensible python-based modeling environment for systems and synthetic biology.
Article in Bio Systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
89 citing papers in PubMed.
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
- Data-driven model reveals increased stability of CAG-expanded huntingtin RNA due to MID1 binding.PLoS computational biology · 2026Article
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- A standardized workflow for kinetic metabolic model curation and dissemination.PLoS computational biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- Spatiotemporal dynamics of Mcl-1 abundance and its influence on apoptosis susceptibility.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the limitations of Bayesian metabolic control analysis.PLoS computational biology · 2026Article
- Verification and reproducible curation of the BioModels repository.PLoS computational biology · 2025Article
- Parameterization of cell-free systems with time-series data using KETCHUP.PLoS computational biology · 2025Article
- GBA Solver: a user-friendly web server for growth balance analysis.Bioinformatics (Oxford, England) · 2025Article
- Digital twin models for predicting venetoclax and azacitidine-induced neutropenia in patients with acute myeloid leukemia.NPJ digital medicine · 2025Article
- A population model reveals a surprising role of stochastic cell division in epigenetic memory systems.iScience · 2025Article
- Maximum likelihood estimation of log-affine models using detailed-balanced reaction networks.Journal of mathematical biology · 2025Article
- SBMLNetwork: A framework for standards-based visualization of biochemical models.PLoS computational biology · 2025Article
- The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions.ACS synthetic biology · 2025Review
- Experimentally Constrained Mechanistic and Data-Driven Models for Simulating NMDA Receptor Dynamics.Biomedicines · 2025Article
- MobsPy: A programming language for biochemical reaction networks.PLoS computational biology · 2025Article
- Speciated evolution of oscillatory mass-action chemical reaction networks.bioRxiv : the preprint server for biology · 2025Article
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
- Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism.NPJ systems biology and applications · 2025Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Here we present Tellurium, a Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source simulation environment composed of multiple libraries, plugins, and specialized modules and methods. Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution. Two interfaces are provided, one based on the Spyder IDE which has an accessible user interface akin to MATLAB and a second based on the Jupyter Notebook, which is a format that contains live code, equations, visualizations, and narrative text. Tellurium uses libRoadRunner as the default SBML simulation engine which supports deterministic simulations, stochastic simulations, and steady-state analyses. Tellurium also includes Antimony, a human-readable model definition language which can be converted to and from SBML. Other standard Python scientific libraries such as NumPy, SciPy, and matplotlib are included by default. Additionally, we include several user-friendly plugins and advanced modules for a wide-variety of applications, ranging from complex algorithms for bifurcation analysis to multidimensional parameter scanning. By combining multiple libraries, plugins, and modules into a single package, Tellurium provides a unified but extensible solution for biological modeling and analysis for both novices and experts. AVAILABILITY: tellurium.analogmachine.org.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.