Methods in cell biology. Volume 110, Computational methods in cell biology /
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...
| Άλλοι συγγραφείς: | , |
|---|---|
| Μορφή: | Ηλ. βιβλίο |
| Γλώσσα: | English |
| Έκδοση: |
Amsterdam :
Elsevier/Academic Press,
c2012.
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| Θέματα: | |
| Διαθέσιμο Online: | Full Text via HEAL-Link |
Πίνακας περιεχομένων:
- Machine generated contents note: I.Introduction / Ambhighainath Ganesan / Andre Mevchenko
- 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
