Machine generated contents note: I. Introduction / Ambhighainath Ganesan / Andre Levchenko -- II. Signaling Systems and Mathematical Models / Ambhighainath Ganesan / Andre Levchenko -- III. Experimentation-aided Model Development / Ambhighainath Ganesan / Andre Levchenko -- IV. Conclusion / Ambhighainath Ganesan / Andre Levchenko -- Acknowledgments / Ambhighainath Ganesan / Andre Levchenko -- References / Ambhighainath Ganesan / Andre Levchenko -- I. Introduction / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- II. Overview of Model/Algorithm / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- III. Biological Insights / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- IV. Open Challenges / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- V.Computational Methods / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- References / Christopher S. Poultney / Alex Greenfield / Richard Bonneau -- I. Introduction / Shao-shan Carol Huang / Ernest Fraenkel -- II.Computational Methods / Shao-shan Carol Huang / Ernest Fraenkel -- III. Biological Insights / Shao-shan Carol Huang / Ernest Fraenkel -- IV. Open Challenges / Shao-shan Carol Huang / Ernest Fraenkel -- Acknowledgments / Shao-shan Carol Huang / Ernest Fraenkel -- References / Shao-shan Carol Huang / Ernest Fraenkel -- I. Introduction / Paul M. Loriaux / Alexander Hoffmann -- II. Overview of Algorithm / Paul M. Loriaux / Alexander Hoffmann -- III. Biological Insights / Paul M. Loriaux / Alexander Hoffmann -- IV. Open Challenges / Paul M. Loriaux / Alexander Hoffmann -- V.Computational Methods / Paul M. Loriaux / Alexander Hoffmann -- Further Reading / Paul M. Loriaux / Alexander Hoffmann -- References / Paul M. Loriaux / Alexander Hoffmann -- I. Introduction / Jacob Stewart-Ornstein / Hana El-Samad -- II. The Need for a Stochastic Modeling Framework / Jacob Stewart-Ornstein / Hana El-Samad -- III. Overview of Computational Approach / Jacob Stewart-Ornstein / Hana El-Samad -- IV. Biological Insights from Computational Approaches / Jacob Stewart-Ornstein / Hana El-Samad -- V.Computational Methods / Jacob Stewart-Ornstein / Hana El-Samad -- VI. Open Challenges / Jacob Stewart-Ornstein / Hana El-Samad -- VII. Conclusions / Jacob Stewart-Ornstein / Hana El-Samad -- References / Jacob Stewart-Ornstein / Hana El-Samad -- Further Reading / Jacob Stewart-Ornstein / Hana El-Samad -- I. Introduction / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- II. Overview of Method / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- III. Biological Insights from Traction Methods / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- IV. Open Challenges / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- V. Methods / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- VI. Summary / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- Acknowledgments / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- References / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- Further Reading / Casey M. Kraning-Rush / Shawn P. Carey / Joseph P. Califano / Cynthia A. Reinhart-King -- I. Introduction / Robert F. Murphy -- II.Components of a Model of Subcellular Organization and Protein Distribution / Robert F. Murphy -- III. Models of Subcellular Organization / Robert F. Murphy -- IV. Protein Distributions Across Subcellular Structures / Robert F. Murphy -- V. Use of Models for Testing Algorithms / Robert F. Murphy -- VI. Conclusion / Robert F. Murphy -- Acknowledgments / Robert F. Murphy -- References / Robert F. Murphy -- I. Introduction / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- II. Overview of Spatial Modeling / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- III. Building a Spatial Model / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- IV. Running Spatial Simulations with VCell: Numerical Method and Simulation Parameters / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- Application to a Specific Example: cAMP Signaling in Neuronal Cells / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- Acknowledgments / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- References / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- Further Reading / Ann E. Cowan / Ion I. Morau / James Schaff / Boris M. Slepehenko / Leslie M. Loew -- I. Introduction / Erik S. Welf / Jason M. Haugh -- II. Model Synthesis / Erik S. Welf / Jason M. Haugh -- III. Model Analysis / Erik S. Welf / Jason M. Haugh -- IV. Biological Insights from the Modeling Approach / Erik S. Welf / Jason M. Haugh -- V. Open Challenges / Erik S. Welf / Jason M. Haugh -- VI.Computational Methods / Erik S. Welf / Jason M. Haugh -- Acknowledgments / Erik S. Welf / Jason M. Haugh -- References / Erik S. Welf / Jason M. Haugh -- I. Introduction / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- II. Overview of the NODE Model / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- III. Biological Insights / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- IV. Open Challenges / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- V.Computational Methods / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- VI. Building a NODE Model / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- VII. Building a Comb Diagram with the NALEDE Extension / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- Further Reading / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- Acknowledgments / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- References / Anil Aswani / Mark D. Biggin / Peter Bickel / Claire Tomlin -- I. Introduction / Tommy Kaplan / Mark D. Biggin -- II. Overview of Model/Algorithm / Tommy Kaplan / Mark D. Biggin -- III. Biological Insights / Tommy Kaplan / Mark D. Biggin -- IV. Open Challenges / Tommy Kaplan / Mark D. Biggin -- V.Computational Methods / Mark D. Biggin / Tommy Kaplan -- VI. Glossary / Tommy Kaplan / Mark D. Biggin -- Further Reading / Tommy Kaplan / Mark D. Biggin -- References / Mark D. Biggin / Tommy Kaplan -- I. Introduction / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- II. Overview of Systems and Methods / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- III. Biological Insights / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- IV. Open Computational Challenges / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- V. Imaging and Computational Methods / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- VI. Further Reading / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- Acknowledgments / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- References / Alexandre Cunha / Paul T. Tarr / Adrienne H.K. Roeder / Alphan Altinok / Eric Mjolsness / Elliot M. Meyerowitz -- I. Introduction / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- II. Glazier-Graner-Hogeweg (GGH) Modeling / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A.

Glazier -- III.CompuCell3D / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- IV. Building CC3D Models / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- V. Conclusion / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- Acknowledgments / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- References / Maciej H. Swat / Gilberto L. Thomas / Julio M. Belmonte / Abbas Shirinifard / Dimitrij Hmeljak / James A. Glazier -- I. Introduction / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- II. Biological Background / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber / Zhiliang Xu / Scott Christley -- III. Overview of the Modeling Approach / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- IV. Study of the Role of the Fibrin Network / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- V. Multiscale Model of Thrombus Development with Fibrin Network Formation / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- VI. GPU Implementation of the Simulation of the Platelet-Blood Flow Interaction / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- VII. Concluding Remarks / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber -- Acknowledgments / Zhiliang Xu / Scott Christley / Joshua Lioi / Oleg Kim / Cameron Harvey / Wenzhao Sun / Elliot D. Rosen / Mark Alber.