Computational Methods in Cell Biology

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...