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Systems biology / edited by Ivan V. Maly.

Contributor(s): Maly, Ivan VMaterial type: TextTextSeries: Methods in molecular biology (Clifton, N.J.) ; v. 500.Publication details: New York : Humana Press, ©2009. Description: 1 online resource (xi, 500 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781934115640; 1934115649; 9781597455251; 1597455253Subject(s): Systems biology | Computational biology | Systems Biology -- methods | Models, Theoretical | Systems Biology | Computational Biology | Systems Biology -- methods | Models, Theoretical | Computational biology | Systems biology | SystembiologieGenre/Form: Electronic books. Additional physical formats: Print version:: Systems biology.DDC classification: 570.285 LOC classification: QH324.2 | .S97 2009NLM classification: W1 | QU 26.5Other classification: Q111 Online resources: Click here to access online
Contents:
Introduction : a practical guide to the systems approach in biology / Ivan V. Maly -- Computational modeling of biochemical networks using COPASI / Pedro Mendes [and others] -- Flux balance analysis : interrogating genome-scale metabolic networks / Matthew A. Oberhardt, Arvind K. Chavali and Jason A. Papin -- Modeling molecular regulatory networks with JigCell and PET / Clifford A. Shaffer [and others] -- Rule-based modeling of biochemical systems with BioNetGen / James R. Faeder, Michael L. Blinov and William S. Hlavacek -- Ingeneue : a software tool to simulate and explore genetic regulatory networks / Kerry J. Kim -- Microfluidics technology for systems biology research / C. Joanne Wang and Andre Levchenko -- Systems approach to therapeutics design / Bert J. Lao and Daniel T. Kamei -- Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models / Jacob Czech, Markus Dittrich, and Joel R. Stiles -- A cell architecture modeling system based on quantitative ultrastructural characteristics / Július Parulek [and others] -- Location proteomics : systematic determination of protein subcellular location / Justin Newberg, Juchang Hua, and Robert F. Murphy -- Model-based global analysis of heterogeneous experimental data using gfit / Mikhail K. Levin [and others] -- Multicell simulations of development and disease using the CompuCell3D simulation environment / Maciej H. Swat [and others] -- BioLogic : a mathematical modeling framework for immunologists / Shlomo Ta'asan and Rima Gandlin -- Dynamic knowledge representation using agent-based modeling : ontology instantiation and verification of conceptual models / Gary An -- Systems biology of microbial communities / Ali Navid [and others].
Summary: The rapidly developing methods of systems biology can help investigators to make inference and predictions from their data that intuition alone would not discern; however, the difficulty lies in the broad knowledge of mathematics and engineering that seems to be required to even evaluate the applicability of the methods to the problem at hand. In Systems Biology, scientists who possess that mathematical knowledge and have applied it effectively to various biological problems contribute methods which reflect their experience, crystallized in a form very similar to typical biological laboratory protocols. In order to best aid researchers, the chapters supply the theory behind the method, its step-by-step implementation, and the pitfalls explained thoroughly and from the practical angle. As a volume of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and easy to use, Systems Biology shatters the perceived insurmountable barrier between the laboratory and systems-biological research techniques.
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Includes bibliographical references and index.

Introduction : a practical guide to the systems approach in biology / Ivan V. Maly -- Computational modeling of biochemical networks using COPASI / Pedro Mendes [and others] -- Flux balance analysis : interrogating genome-scale metabolic networks / Matthew A. Oberhardt, Arvind K. Chavali and Jason A. Papin -- Modeling molecular regulatory networks with JigCell and PET / Clifford A. Shaffer [and others] -- Rule-based modeling of biochemical systems with BioNetGen / James R. Faeder, Michael L. Blinov and William S. Hlavacek -- Ingeneue : a software tool to simulate and explore genetic regulatory networks / Kerry J. Kim -- Microfluidics technology for systems biology research / C. Joanne Wang and Andre Levchenko -- Systems approach to therapeutics design / Bert J. Lao and Daniel T. Kamei -- Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models / Jacob Czech, Markus Dittrich, and Joel R. Stiles -- A cell architecture modeling system based on quantitative ultrastructural characteristics / Július Parulek [and others] -- Location proteomics : systematic determination of protein subcellular location / Justin Newberg, Juchang Hua, and Robert F. Murphy -- Model-based global analysis of heterogeneous experimental data using gfit / Mikhail K. Levin [and others] -- Multicell simulations of development and disease using the CompuCell3D simulation environment / Maciej H. Swat [and others] -- BioLogic : a mathematical modeling framework for immunologists / Shlomo Ta'asan and Rima Gandlin -- Dynamic knowledge representation using agent-based modeling : ontology instantiation and verification of conceptual models / Gary An -- Systems biology of microbial communities / Ali Navid [and others].

The rapidly developing methods of systems biology can help investigators to make inference and predictions from their data that intuition alone would not discern; however, the difficulty lies in the broad knowledge of mathematics and engineering that seems to be required to even evaluate the applicability of the methods to the problem at hand. In Systems Biology, scientists who possess that mathematical knowledge and have applied it effectively to various biological problems contribute methods which reflect their experience, crystallized in a form very similar to typical biological laboratory protocols. In order to best aid researchers, the chapters supply the theory behind the method, its step-by-step implementation, and the pitfalls explained thoroughly and from the practical angle. As a volume of the highly successful Methods in Molecular Biology series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and easy to use, Systems Biology shatters the perceived insurmountable barrier between the laboratory and systems-biological research techniques.

English.

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