Contents
About the Special Issue Editors ..................................... vii
Ross P. Carlson and Herbert M. Sauro
Special Issue: Methods in Computational Biology
Reprinted from: Processes 2019, 7, 205, doi:10.3390/pr7040205 ..................... 1
Veronica L. Porubsky and Herbert M. Sauro
Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using
Python
Reprinted from: Processes 2019, 7, 163, doi:10.3390/pr7030163 ..................... 4
Poonam Phalak and Michael A. Henson
Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota
Reprinted from: Processes 2019, 7, 97, doi:10.3390/pr7020097 ..................... 21
Kerri-Ann Norton, Chang Gong, Samira Jamalian and Aleksander S. Popel
Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment
Reprinted from: Processes 2019, 7, 37, doi:10.3390/pr7010037 ..................... 41
Andr´ e H. Erhardt
Early Afterdepolarisations Induced by an Enhancement in the Calcium Current
Reprinted from: Processes 2019, 7, 20, doi:10.3390/pr7010020 ..................... 64
Frances Pool, Peter K. Sweby and Marcus J. Tindall
An Integrated Mathematical Model of Cellular Cholesterol Biosynthesis and
Lipoprotein Metabolism
Reprinted from: Processes 2018, 6, 134, doi:10.3390/pr6080134 ..................... 80
Parham Farzan and Marianthi G. Ierapetritou
A Framework for the Development of Integrated and Computationally Feasible Models of
Large-Scale Mammalian Cell Bioreactors
Reprinted from: Processes 2018, 6, 82, doi:10.3390/pr6070082 .....................114
Justin T. Roberts, Dillon G. Patterson, Valeria M. King, Shivam V. Amin, Caroline J. Polska,
Dominika Houserova, Aline Crucello, Emmaline C. Barnhill, Molly M. Miller,
Timothy D. Sherman and Glen M. Borchert
ADAR Mediated RNA Editing Modulates MicroRNA Targeting in Human Breast Cancer
Reprinted from: Processes 2018, 6, 42, doi:10.3390/pr6050042 .....................130
Tim Daniel Rose and Jean-Pierre Mazat
FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks
Reprinted from: Processes 2018, 6, 39, doi:10.3390/pr6050039 .....................144
Ashley E. Beck, Kristopher A. Hunt and Ross P. Carlson
Measuring Cellular Biomass Composition for Computational Biology Applications
Reprinted from: Processes 2018, 6, 38, doi:10.3390/pr6050038 .....................154
C. Anthony Hunt, Ahmet Erdemir, William W. Lytton, Feilim Mac Gabhann,
Edward A. Sander, Mark K. Transtrum and Lealem Mulugeta
The Spectrum of Mechanism-Oriented Models and Methods for Explanations of
Biological Phenomena
Reprinted from: Processes 2018, 6, 56, doi:10.3390/pr6050056 .....................181
v
About the Special Issue Editors ..................................... vii
Ross P. Carlson and Herbert M. Sauro
Special Issue: Methods in Computational Biology
Reprinted from: Processes 2019, 7, 205, doi:10.3390/pr7040205 ..................... 1
Veronica L. Porubsky and Herbert M. Sauro
Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using
Python
Reprinted from: Processes 2019, 7, 163, doi:10.3390/pr7030163 ..................... 4
Poonam Phalak and Michael A. Henson
Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota
Reprinted from: Processes 2019, 7, 97, doi:10.3390/pr7020097 ..................... 21
Kerri-Ann Norton, Chang Gong, Samira Jamalian and Aleksander S. Popel
Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment
Reprinted from: Processes 2019, 7, 37, doi:10.3390/pr7010037 ..................... 41
Andr´ e H. Erhardt
Early Afterdepolarisations Induced by an Enhancement in the Calcium Current
Reprinted from: Processes 2019, 7, 20, doi:10.3390/pr7010020 ..................... 64
Frances Pool, Peter K. Sweby and Marcus J. Tindall
An Integrated Mathematical Model of Cellular Cholesterol Biosynthesis and
Lipoprotein Metabolism
Reprinted from: Processes 2018, 6, 134, doi:10.3390/pr6080134 ..................... 80
Parham Farzan and Marianthi G. Ierapetritou
A Framework for the Development of Integrated and Computationally Feasible Models of
Large-Scale Mammalian Cell Bioreactors
Reprinted from: Processes 2018, 6, 82, doi:10.3390/pr6070082 .....................114
Justin T. Roberts, Dillon G. Patterson, Valeria M. King, Shivam V. Amin, Caroline J. Polska,
Dominika Houserova, Aline Crucello, Emmaline C. Barnhill, Molly M. Miller,
Timothy D. Sherman and Glen M. Borchert
ADAR Mediated RNA Editing Modulates MicroRNA Targeting in Human Breast Cancer
Reprinted from: Processes 2018, 6, 42, doi:10.3390/pr6050042 .....................130
Tim Daniel Rose and Jean-Pierre Mazat
FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks
Reprinted from: Processes 2018, 6, 39, doi:10.3390/pr6050039 .....................144
Ashley E. Beck, Kristopher A. Hunt and Ross P. Carlson
Measuring Cellular Biomass Composition for Computational Biology Applications
Reprinted from: Processes 2018, 6, 38, doi:10.3390/pr6050038 .....................154
C. Anthony Hunt, Ahmet Erdemir, William W. Lytton, Feilim Mac Gabhann,
Edward A. Sander, Mark K. Transtrum and Lealem Mulugeta
The Spectrum of Mechanism-Oriented Models and Methods for Explanations of
Biological Phenomena
Reprinted from: Processes 2018, 6, 56, doi:10.3390/pr6050056 .....................181
v