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...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Asthagiri, Anand R., 1974-, Arkin, Adam, 1966-
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Amsterdam : Elsevier/Academic Press, �2012.
Colección:Methods in cell biology ; v. 110.
Temas:
Cytology > Computer simulation.
Cytology > Data processing.
Cytology.
Cell Biology
Cytology
Cytologie > Simulation par ordinateur.
Cytologie > Informatique.
Cytologie.
SCIENCE > Mife Sciences > Cell Biology.
Cytology > Computer simulation
Cytology > Data processing
bioinformatics
celbiologie
cellular biology
computers
computational science
computersimulatie
computer simulation
modellen
models
cellen
cells
Bioinformatics (General)
Cellular Biology
Bioinformatica (algemeen)
Celbiologie
Acceso en línea:Texto completo
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Tabla de Contenidos:
  • 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.

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