Bibliothèque de L'IMIST/CNRST

Includes bibliographical references and index.

Computational methods are playing an ever increasing role in cell biology. This volume of Methods in Cell Biology focuses on Computational Methods in Cell Biology and consists of two parts: (1) data extraction and analysis to distill models and mechanisms, and (2) developing and simulating models to make predictions and testable hypotheses. Focuses on computational methods in cell biologySplit into 2 parts--data extraction and analysis to distill models and mechanisms, and developing and simulating models to make predictions and testable hypothesesEmphasizes the intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment.

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 --