Tellurium: An extensible python-based modeling environment for systems and synthetic biology

Kiri Choi, Kyle Medley, Matthias König, +4

Biosystems

BiologyEngineeringComplex Biological SystemComputational BiologySynthetic Biology +7

libRoadRunner: a high performance SBML simulation and analysis library

Endre Somogyi, Jean‐Marie C. Bouteiller, James A. Glazier, +4

Bioinformatics

Toward Community Standards and Software for Whole-Cell Modeling

Dagmar Waltemath, Jonathan R. Karr, Frank Bergmann, +53

IEEE Transactions on Biomedical Engineering

Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity

Shaolei Xiong, Wei Wang, Alexander Kenzior, +12

Current Biology

BiologyNutritionFood ScarcityPhysiologyLipid Science +5

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

Kyle Medley, Kiri Choi, Matthias König, +5

PLoS Computational Biology

The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites

Kyle Medley, Jenna L. Persons, Tathagata Biswas, +5

eLife

Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility

Luke Olsen, Michaella J. Levy, Kyle Medley, +17

Proceedings of the National Academy of Sciences

Guidelines for Reproducibly Building and Simulating Systems Biology Models

Kyle Medley, Arthur P. Goldberg, Jonathan R. Karr

IEEE Transactions on Biomedical Engineering

Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

Kiri Choi, Kyle Medley, Caroline Cannistra, +4

EngineeringSimulationSoftware AnalysisReproducibility PlatformModeling And Simulation +22

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML

Kiri Choi, Lucian P. Smith, Kyle Medley, +1

Journal of Bioinformatics and Computational Biology