MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework von Tapia, Jose-Juan, Saglam, Ali Sinan, Czech, Jacob, Kuczewski, Robert, Bartol, Thomas M., Sejnowski, Terrence J., Faeder, James R.

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CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations von Majarian, Timothy D., Cao-Berg, Ivan, Ruan, Xiongtao, Murphy, Robert F.

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Using rxncon to Develop Rule-Based Models von Romers, Jesper, Thieme, Sebastian, Münzner, Ulrike, Krantz, Marcus

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A Step-by-Step Guide to Using BioNetFit von Hlavacek, William S., Csicsery-Ronay, Jennifer A., Baker, Lewis R., Ramos Álamo, María del Carmen, Ionkov, Alexander, Mitra, Eshan D., Suderman, Ryan, Erickson, Keesha E., Dias, Raquel, Colvin, Joshua, Thomas, Brandon R., Posner, Richard G.

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Markov Chain Aggregation and Its Application to Rule-Based Modelling von Petrov, Tatjana

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RKappa: Software for Analyzing Rule-Based Models von Sorokin, Anatoly, Sorokina, Oksana, Douglas Armstrong, J.

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Using Python for Spatially Resolved Modeling with Simmune von Angermann, Bastian R., Meier-Schellersheim, Martin

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Rule-Based Modeling Using Wildcards in the Smoldyn Simulator von Andrews, Steven S.

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Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB) von Palmisano, Alida, Hoops, Stefan, Watson, Layne T., Jones, Thomas C., Tyson, John J., Shaffer, Clifford A.

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In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics von Feng, Song, Soyer, Orkun S.

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Recipes for Analysis of Molecular Networks Using the Data2Dynamics Modeling Environment von Steiert, Bernhard, Kreutz, Clemens, Raue, Andreas, Timmer, Jens

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Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules von Suderman, Ryan, Fricke, G. Matthew, Hlavacek, William S.

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Using Mechanistic Models for Analysis of Proteomic Data von Chylek, Lily A.

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Spatial Rule-Based Simulations: The SRSim Software von Henze, Richard, Grünert, Gerd, Ibrahim, Bashar, Dittrich, Peter

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A Pycellerator Tutorial von Shapiro, Bruce E., Mjolsness, Eric

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Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules von Helms, Tobias, Warnke, Tom, Uhrmacher, Adelinde M.

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Shaken Snow Globes: Kinematic Tracers of the Multiphase Condensation Cascade in Massive Galaxies, Groups, and Clusters von Gaspari, M., McDonald, M., Hamer, S. L., Brighenti, F., Temi, P., Gendron-Marsolais, M., Hlavacek-Larrondo, J., Edge, A. C., Werner, N., Tozzi, P., Sun, M., Stone, J. M., Tremblay, G. R., Hogan, M. T., Eckert, D., Ettori, S., Yu, H., Biffi, V., Planelles, S.

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Mitochondrial morphological features are associated with fission and fusion events von Westrate, Laura M, Drocco, Jeffrey A, Martin, Katie R, Hlavacek, William S, MacKeigan, Jeffrey P

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The Utility of CT Angiography in Neonates with Pulmonary Atresia with Intact Ventricular Septum and Concern for Right Ventricular Dependent Coronary Circulation: Case Series von Boucek, Katerina, Hlavacek, Anthony

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The Remarkable Similarity of Massive Galaxy Clusters from z ∼ 0 to z ∼ 1.9 von McDonald, M., Allen, S. W., Bayliss, M., Benson, B. A., Bleem, L. E., Brodwin, M., Bulbul, E., Carlstrom, J. E., Forman, W. R., Hlavacek-Larrondo, J., Garmire, G. P., Gaspari, M., Gladders, M. D., Mantz, A. B., Murray, S. S.

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