Logical Modeling Of Cellular Processes From Software Development To Network Dynamics

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Logical Modeling of Cellular Processes: From Software Development to Network Dynamics

Matteo Barberis,Tomáš Helikar
Logical Modeling of Cellular Processes From Software Development to Network Dynamics Book PDF

Author : Matteo Barberis,Tomáš Helikar
Publisher : Frontiers Media SA
Page : 340 pages
File Size : 46,5 Mb
Release : 2019-08-16
Category : Electronic
ISBN : 9782889459834

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Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by Matteo Barberis,Tomáš Helikar Pdf

Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

Physics of Molecular and Cellular Processes

Krastan B. Blagoev,Herbert Levine
Physics of Molecular and Cellular Processes Book PDF

Author : Krastan B. Blagoev,Herbert Levine
Publisher : Springer Nature
Page : 265 pages
File Size : 53,9 Mb
Release : 2022-09-08
Category : Science
ISBN : 9783030986063

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Physics of Molecular and Cellular Processes by Krastan B. Blagoev,Herbert Levine Pdf

This is a graduate-level introduction to quantitative concepts and methods in the science of living systems. It relies on a systems approach for understanding the physical principles operating in biology. Physical phenomena are treated at the appropriate spatio-temporal scale and phenomenological equations are used in order to reflect the system of interest. Biological details enter to the degree necessary for understanding specific processes, but in many cases the approach is not reductionist. This is in line with the approach taken by physics to many other complex systems. The book bridges the gap between graduate students’ general physics courses and research papers published in professional journals. It gives students the foundations needed for independent research in biological physics and for working in collaborations aimed at quantitative biology and biomedical research. Also included are modern mathematical and theoretical physics methods, giving the student a broad knowledge of tools that can shed light on the sophisticated mechanisms brought forth by evolution in biological systems. The content covers many aspects that have been the focus of active research over the past twenty years, reflecting the authors' experience as leading researchers and teachers in this field.

New Methods and Paradigms for Modeling Dynamic Processes Based on Cellular Automata

Bilan, Stepan Mykolayovych,Bilan, Mykola Mykolayovych,Motornyuk, Ruslan Leonidovich
New Methods and Paradigms for Modeling Dynamic Processes Based on Cellular Automata Book PDF

Author : Bilan, Stepan Mykolayovych,Bilan, Mykola Mykolayovych,Motornyuk, Ruslan Leonidovich
Publisher : IGI Global
Page : 326 pages
File Size : 40,6 Mb
Release : 2020-10-16
Category : Computers
ISBN : 9781799826514

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New Methods and Paradigms for Modeling Dynamic Processes Based on Cellular Automata by Bilan, Stepan Mykolayovych,Bilan, Mykola Mykolayovych,Motornyuk, Ruslan Leonidovich Pdf

The accelerating development of computer technology and communications can replace many of the functions of human intellectual activity, as well as help them in making decisions in various situations of their lives. To implement intelligent functions for various purposes, numerous models, paradigms, architectures, and hardware and software are being developed. Because the world is constantly evolving, there is a need to constantly study various dynamic processes to determine possible negative situations that can lead to undesirable catastrophic phenomena and changes. Recently, more attention has been paid to the study of natural processes in nature. Scientific works are appearing that describe the behavior and development of living organisms and the processes of their interaction. Cellular automata are increasingly used to describe and model them. New Methods and Paradigms for Modeling Dynamic Processes Based on Cellular Automata is a collection of innovative research that describes the models and paradigms of building cellular automata that allows for the simulation of the dynamics of the interaction of living organisms from a different scientific point of view. For this, asynchronous cellular automata with a dynamically changing number of “living” cells are used. The chapters describe the theoretical concepts of constructing asynchronous cellular automata with active cells. Much attention is paid to the use of the proposed theoretical principles for solving modeling problems and solving specific applied problems of forming pseudorandom sequences and image processing based on modeling of the human visual channel. Featuring research on topics such as colony interaction, image processing and recognition, and influence mode, this book is ideally designed for engineers, programmers, software developers, researchers, academicians, and students.

Comprehensive Toxicology

Anonim
Comprehensive Toxicology Book PDF

Author : Anonim
Publisher : Elsevier
Page : 8639 pages
File Size : 50,7 Mb
Release : 2017-12-01
Category : Science
ISBN : 9780081006122

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Comprehensive Toxicology by Anonim Pdf

Comprehensive Toxicology, Third Edition, Fifteen Volume Set discusses chemical effects on biological systems, with a focus on understanding the mechanisms by which chemicals induce adverse health effects. Organized by organ system, this comprehensive reference work addresses the toxicological effects of chemicals on the immune system, the hematopoietic system, cardiovascular system, respiratory system, hepatic toxicology, renal toxicology, gastrointestinal toxicology, reproductive and endocrine toxicology, neuro and behavioral toxicology, developmental toxicology and carcinogenesis, also including critical sections that cover the general principles of toxicology, cellular and molecular toxicology, biotransformation and toxicology testing and evaluation. Each section is examined in state-of-the-art chapters written by domain experts, providing key information to support the investigations of researchers across the medical, veterinary, food, environment and chemical research industries, and national and international regulatory agencies. Thoroughly revised and expanded to 15 volumes that include the latest advances in research, and uniquely organized by organ system for ease of reference and diagnosis, this new edition is an essential reference for researchers of toxicology. Organized to cover both the fundamental principles of toxicology and unique aspects of major organ systems Thoroughly revised to include the latest advances in the toxicological effects of chemicals on the immune system Features additional coverage throughout and a new volume on toxicology of the hematopoietic system Presents in-depth, comprehensive coverage from an international author base of domain experts

Logical Modeling of Biological Systems

Luis Fariñas del Cerro,Katsumi Inoue
Logical Modeling of Biological Systems Book PDF

Author : Luis Fariñas del Cerro,Katsumi Inoue
Publisher : John Wiley & Sons
Page : 328 pages
File Size : 41,8 Mb
Release : 2014-08-08
Category : Science
ISBN : 9781119015215

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Logical Modeling of Biological Systems by Luis Fariñas del Cerro,Katsumi Inoue Pdf

Systems Biology is the systematic study of the interactions between the components of a biological system and studies how these interactions give rise to the function and behavior of the living system. Through this, a life process is to be understood as a whole system rather than the collection of the parts considered separately. Systems Biology is therefore more than just an emerging field: it represents a new way of thinking about biology with a dramatic impact on the way that research is performed. The logical approach provides an intuitive method to provide explanations based on an expressive relational language. This book covers various aspects of logical modeling of biological systems, bringing together 10 recent logic-based approaches to Systems Biology by leading scientists. The chapters cover the biological fields of gene regulatory networks, signaling networks, metabolic pathways, molecular interaction and network dynamics, and show logical methods for these domains based on propositional and first-order logic, logic programming, answer set programming, temporal logic, Boolean networks, Petri nets, process hitting, and abductive and inductive logic programming. It provides an excellent guide for all scientists, biologists, bioinformaticians, and engineers, who are interested in logic-based modeling of biological systems, and the authors hope that new scientists will be encouraged to join this exciting scientific endeavor.

Computational Biology for Stem Cell Research

Pawan Raghav,Rajesh Kumar,Anjali Lathwal,Navneet Sharma
Computational Biology for Stem Cell Research Book PDF

Author : Pawan Raghav,Rajesh Kumar,Anjali Lathwal,Navneet Sharma
Publisher : Elsevier
Page : 568 pages
File Size : 47,7 Mb
Release : 2024-01-12
Category : Science
ISBN : 9780443132216

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Computational Biology for Stem Cell Research by Pawan Raghav,Rajesh Kumar,Anjali Lathwal,Navneet Sharma Pdf

Computational Biology for Stem Cell Research is an invaluable guide for researchers as they explore HSCs and MSCs in computational biology. With the growing advancement of technology in the field of biomedical sciences, computational approaches have reduced the financial and experimental burden of the experimental process. In the shortest span, it has established itself as an integral component of any biological research activity. HSC informatics (in silico) techniques such as machine learning, genome network analysis, data mining, complex genome structures, docking, system biology, mathematical modeling, programming (R, Python, Perl, etc.) help to analyze, visualize, network constructions, and protein-ligand or protein-protein interactions. This book is aimed at beginners with an exact correlation between the biomedical sciences and in silico computational methods for HSCs transplantation and translational research and provides insights into methods targeting HSCs properties like proliferation, self-renewal, differentiation, and apoptosis. Modeling Stem Cell Behavior: Explore stem cell behavior through animal models, bridging laboratory studies to real-world clinical allogeneic HSC transplantation (HSCT) scenarios. Bioinformatics-Driven Translational Research: Navigate a path from bench to bedside with cutting-edge bioinformatics approaches, translating computational insights into tangible advancements in stem cell research and medical applications. Interdisciplinary Resource: Discover a single comprehensive resource catering to biomedical sciences, life sciences, and chemistry fields, offering essential insights into computational tools vital for modern research.

Integration of Omics Approaches and Systems Biology for Clinical Applications

Antonia Vlahou,Fulvio Magni,Harald Mischak,Jerome Zoidakis
Integration of Omics Approaches and Systems Biology for Clinical Applications Book PDF

Author : Antonia Vlahou,Fulvio Magni,Harald Mischak,Jerome Zoidakis
Publisher : John Wiley & Sons
Page : 384 pages
File Size : 50,6 Mb
Release : 2018-01-24
Category : Science
ISBN : 9781119183976

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Integration of Omics Approaches and Systems Biology for Clinical Applications by Antonia Vlahou,Fulvio Magni,Harald Mischak,Jerome Zoidakis Pdf

Introduces readers to the state of the art of omics platforms and all aspects of omics approaches for clinical applications This book presents different high throughput omics platforms used to analyze tissue, plasma, and urine. The reader is introduced to state of the art analytical approaches (sample preparation and instrumentation) related to proteomics, peptidomics, transcriptomics, and metabolomics. In addition, the book highlights innovative approaches using bioinformatics, urine miRNAs, and MALDI tissue imaging in the context of clinical applications. Particular emphasis is put on integration of data generated from these different platforms in order to uncover the molecular landscape of diseases. The relevance of each approach to the clinical setting is explained and future applications for patient monitoring or treatment are discussed. Integration of omics Approaches and Systems Biology for Clinical Applications presents an overview of state of the art omics techniques. These methods are employed in order to obtain the comprehensive molecular profile of biological specimens. In addition, computational tools are used for organizing and integrating these multi-source data towards developing molecular models that reflect the pathophysiology of diseases. Investigation of chronic kidney disease (CKD) and bladder cancer are used as test cases. These represent multi-factorial, highly heterogeneous diseases, and are among the most significant health issues in developed countries with a rapidly aging population. The book presents novel insights on CKD and bladder cancer obtained by omics data integration as an example of the application of systems biology in the clinical setting. Describes a range of state of the art omics analytical platforms Covers all aspects of the systems biology approach—from sample preparation to data integration and bioinformatics analysis Contains specific examples of omics methods applied in the investigation of human diseases (Chronic Kidney Disease, Bladder Cancer) Integration of omics Approaches and Systems Biology for Clinical Applications will appeal to a wide spectrum of scientists including biologists, biotechnologists, biochemists, biophysicists, and bioinformaticians working on the different molecular platforms. It is also an excellent text for students interested in these fields.

Computer Aided Verification

Alexandra Silva,K. Rustan M. Leino
Computer Aided Verification Book PDF

Author : Alexandra Silva,K. Rustan M. Leino
Publisher : Springer Nature
Page : 922 pages
File Size : 53,5 Mb
Release : 2021-07-17
Category : Computers
ISBN : 9783030816858

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Computer Aided Verification by Alexandra Silva,K. Rustan M. Leino Pdf

This open access two-volume set LNCS 12759 and 12760 constitutes the refereed proceedings of the 33rd International Conference on Computer Aided Verification, CAV 2021, held virtually in July 2021. The 63 full papers presented together with 16 tool papers and 5 invited papers were carefully reviewed and selected from 290 submissions. The papers were organized in the following topical sections: Part I: invited papers; AI verification; concurrency and blockchain; hybrid and cyber-physical systems; security; and synthesis. Part II: complexity and termination; decision procedures and solvers; hardware and model checking; logical foundations; and software verification. This is an open access book.

The Logic of Adaptive Behavior

Martijn van Otterlo
The Logic of Adaptive Behavior Book PDF

Author : Martijn van Otterlo
Publisher : IOS Press
Page : 508 pages
File Size : 42,9 Mb
Release : 2009
Category : Business & Economics
ISBN : 9781586039691

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The Logic of Adaptive Behavior by Martijn van Otterlo Pdf

Markov decision processes have become the de facto standard in modeling and solving sequential decision making problems under uncertainty. This book studies lifting Markov decision processes, reinforcement learning and dynamic programming to the first-order (or, relational) setting.

Computer Methods Part B

Anonim
Computer Methods Part B Book PDF

Author : Anonim
Publisher : Academic Press
Page : 711 pages
File Size : 40,7 Mb
Release : 2009-11-05
Category : Computers
ISBN : 9780080962801

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Computer Methods Part B by Anonim Pdf

The combination of faster, more advanced computers and more quantitatively oriented biomedical researchers has recently yielded new and more precise methods for the analysis of biomedical data. These better analyses have enhanced the conclusions that can be drawn from biomedical data, and they have changed the way that experiments are designed and performed. This volume, along with previous and forthcoming Computer Methods volumes for the Methods in Enzymology serial, aims to inform biomedical researchers about recent applications of modern data analysis and simulation methods as applied to biomedical research. Presents step-by-step computer methods and discusses the techniques in detail to enable their implementation in solving a wide range of problems Informs biomedical researchers of the modern data analysis methods that have developed alongside computer hardware Presents methods at the "nuts and bolts" level to identify and resolve a problem and analyze what the results mean

Encyclopedia of Bioinformatics and Computational Biology

Anonim
Encyclopedia of Bioinformatics and Computational Biology Book PDF

Author : Anonim
Publisher : Elsevier
Page : 3421 pages
File Size : 46,5 Mb
Release : 2018-08-21
Category : Medical
ISBN : 9780128114322

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Encyclopedia of Bioinformatics and Computational Biology by Anonim Pdf

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Current Challenges in Modeling Cellular Metabolism

Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård
Current Challenges in Modeling Cellular Metabolism Book PDF

Author : Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård
Publisher : Frontiers Media SA
Page : 117 pages
File Size : 49,7 Mb
Release : 2016-01-21
Category : Biology (General)
ISBN : 9782889197545

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Current Challenges in Modeling Cellular Metabolism by Daniel Machado,Kai H. Zhuang,Nikolaus Sonnenschein,Markus J. Herrgård Pdf

Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.

Understanding the Dynamics of Biological Systems

Werner Dubitzky,Jennifer Southgate,Hendrik Fuß
Understanding the Dynamics of Biological Systems Book PDF

Author : Werner Dubitzky,Jennifer Southgate,Hendrik Fuß
Publisher : Springer Science & Business Media
Page : 249 pages
File Size : 44,7 Mb
Release : 2011-01-07
Category : Science
ISBN : 9781441979643

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Understanding the Dynamics of Biological Systems by Werner Dubitzky,Jennifer Southgate,Hendrik Fuß Pdf

This book is intended as a communication platform to bridge the cultural, conceptual, and technological gap among the key systems biology disciplines of biology, mathematics, and information technology. To support this goal, contributors were asked to adopts an approach that appeals to audiences from different backgrounds.

Programming Logics

Andrei Voronkov,Christoph Weidenbach
Programming Logics Book PDF

Author : Andrei Voronkov,Christoph Weidenbach
Publisher : Springer
Page : 447 pages
File Size : 51,9 Mb
Release : 2013-04-05
Category : Mathematics
ISBN : 9783642376511

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Programming Logics by Andrei Voronkov,Christoph Weidenbach Pdf

This Festschrift volume, published in memory of Harald Ganzinger, contains 17 papers from colleagues all over the world and covers all the fields to which Harald Ganzinger dedicated his work during his academic career. The volume begins with a complete account of Harald Ganzinger's work and then turns its focus to the research of his former colleagues, students, and friends who pay tribute to him through their writing. Their individual papers span a broad range of topics, including programming language semantics, analysis and verification, first-order and higher-order theorem proving, unification theory, non-classical logics, reasoning modulo theories, and applications of automated reasoning in biology.

Computational Methods in Systems Biology

Olivier Roux,Jérémie Bourdon
Computational Methods in Systems Biology Book PDF

Author : Olivier Roux,Jérémie Bourdon
Publisher : Springer
Page : 288 pages
File Size : 46,6 Mb
Release : 2015-09-01
Category : Computers
ISBN : 9783319234014

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Computational Methods in Systems Biology by Olivier Roux,Jérémie Bourdon Pdf

This book constitutes the refereed proceedings of the 13th International Conference on Computational Methods in Systems Biology, CMSB 2015, held in Nantes, France, in September 2015. The 20 full papers and 2 short papers presented were carefully reviewed and selected from 43 full and 4 short paper submissions. The papers cover a wide range of topics in the analysis of biological systems, networks and data such as model checking, stochastic analysis, hybrid systems, circadian clock, time series data, logic programming, and constraints solving ranging from intercellular to multiscale.