Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process. This book wants to address four main issues related to the building and validation of computational models of biomedical processes: 1. Modeling establishment under uncertainty 2. Model selection and parameter fitting 3. Sensitivity analysis and model adaptation 4. Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples. This book is intended for graduate students and researchers active in the field of computational modeling of biomedical processes who seek to acquaint themselves with the different ways in which to study the parameter space of their model as well as its overall behavior.
Anti-evolutionists, climate denialists, and anti-vaxxers, among others, question some of the best-established scientific findings by referring to the uncertainties in these areas of research. Uncertainty: How It Makes Science Advance shows that uncertainty is an inherent feature of science that makes it advance by motivating further research.
An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid
This volume covers a wide range of topics concerning methodological, epistemological, and regulatory-ethical issues around pharmacology. The book focuses in particular on the diverse sources of uncertainty, the different kinds of uncertainty that there are, and the diverse ways in which these uncertainties are (or could be) addressed. Compared with the more basic sciences, such as chemistry or biology, pharmacology works across diverse observable levels of reality: although the first step in the causal chain leading to the therapeutic outcome takes place at the biochemical level, the end-effect is a clinically observable result—which is influenced not only by biological actions, but also psychological and social phenomena. Issues of causality and evidence must be treated with these specific aspects in mind. In covering these issues, the book opens up a common domain of investigation which intersects the deeply intertwined dimensions of pharmacological research, pharmaceutical regulation and the related economic environment. The book is a collective endeavour with in-depth contributions from experts in pharmacology, philosophy of medicine, statistics, scientific methodology, formal and social epistemology, working in constant dialogue across disciplinary boundaries.
This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
Modeling and Inverse Problems in the Presence of Uncertainty collects recent research-including the authors' own substantial projects-on uncertainty propagation and quantification. It covers two sources of uncertainty: where uncertainty is present primarily due to measurement errors and where uncertainty is present due to the modeling formulation i
It is now becoming recognized in the measurement community that it is as important to communicate the uncertainty related to a specific measurement as it is to report the measurement itself. Without knowing the uncertainty, it is impossible for the users of the result to know what confidence can be placed in it; it is also impossible to assess the comparability of different measurements of the same parameter. This volume collects 20 outstanding papers on the topic, mostly published from 1999-2002 in the journal "Accreditation and Quality Assurance." They provide the rationale for why it is important to evaluate and report the uncertainty of a result in a consistent manner. They also describe the concept of uncertainty, the methodology for evaluating uncertainty, and the advantages of using suitable reference materials. Finally, the benefits to both the analytical laboratory and the user of the results are considered.
This set of lecture notes gives a first coherent account of a novel aspect of the living world that can be called biological information. The book presents both a pedagogical and state-of-the art roadmap of this rapidly evolving area and covers the whole field, from information which is encoded in the molecular genetic code to the description of large-scale evolution of complex species networks. The book will prove useful for all those who work at the interface of biology, physics and information science.
