Dynamic Systems Biology Modeling and Simulation

Academic Press
1
Free sample

Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author’s own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications.
  • Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics; PLUS .......
  • The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of “math modeling” with life sciences.
  • Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization.
  • Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models.
  • A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course.

Importantly, the slides are editable, so they can be readily adapted to a lecturer’s personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content.

The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: joed@cs.ucla.edu

Read more

About the author

“Professor Joe” - as he is called by his students - is a Distinguished Professor of Computer Science and Medicine and Chair of the Computational & Systems Biology Interdepartmental Program at UCLA - an undergraduate research-oriented program he nurtured and honed over several decades. As an active full-time member of the UCLA faculty for nearly half a century, he also developed and led innovative graduate PhD programs, including Computational Systems Biology in Computer Science, and Biosystem Science and Engineering in Biomedical Engineering. He has mentored students from these programs since 1968, as Director of the UCLA Biocybernetics Laboratory, and was awarded the prestigious UCLA Distinguished Teaching Award and Eby Award for Creative Teaching in 2003, and the Lockeed-Martin Award for Teaching Excellence in 2004. Professor Joe also is a Fellow of the Biomedical Engineering Society. Visiting professorships included stints at universities in Canada, Italy, Sweden and the UK and he was a Senior Fulbright-Hays Scholar in Italy in 1979.

Professor Joe has been very active in the publishing world. As an editor, he founded and was Editor-in-Chief of the Modeling Methodology Forum - a department in seven of the American Journals of Physiology - from 1984 thru 1991. As a writer, he authored or coauthored both editions of Feedback and Control Systems (Schaum-McGraw-Hill 1967 and 1990), more than 200 research articles, and recently published his opus textbook: Dynamic Systems Biology Modeling and Simulation (Academic Press/Elsevier November 2013 and February 2014).

Much of his research has been based on integrating experimental neuroendocrine and metabolism studies in mammals and fishes with data-driven mathematical modeling methodology - strongly motivated by his experiences in “wet-lab”. His seminal contributions to modeling theory and practice are in structural identifiability (parameter ambiguity) analysis, driven by experimental encumbrances. He introduced the notions of interval and quasi-identifiablity of unidentifiable dynamic system models, and his lab has developed symbolic algorithmic approaches and new internet software (web app COMBOS) for computing identifiable parameter combinations. These are the aggregate parts of otherwise unidentifiable models that can be quantified - with broad application in model reduction (simplification) and experiment design. His long-term contributions to quantitative understanding of thyroid hormone production and metabolism in mammals and fishes have recently been crystallized into web app THYROSIM - for internet-based research and teaching about thyroid hormone dynamics in humans.

Last but not least, Professor Joe is a passionate straight-ahead jazz saxophone player (alto and tenor), an alternate career begun in the 1950s in NYC at Stuyvesant High School - temporarily suspended when he started undergrad school, and resumed again in middle-age. He recently added flute to his practice schedule and he and his band - Acoustically Speaking -can be found occasionally gigging in Los Angeles or Honolulu haunts.

Read more
5.0
1 total
Loading...

Additional Information

Publisher
Academic Press
Read more
Published on
Jan 10, 2015
Read more
Pages
884
Read more
ISBN
9780124104938
Read more
Language
English
Read more
Genres
Computers / Data Modeling & Design
Science / Life Sciences / Ecology
Science / Life Sciences / General
Read more
Content Protection
This content is DRM protected.
Read more
Read Aloud
Available on Android devices
Read more
Eligible for Family Library

Reading information

Smartphones and Tablets

Install the Google Play Books app for Android and iPad/iPhone. It syncs automatically with your account and allows you to read online or offline wherever you are.

Laptops and Computers

You can read books purchased on Google Play using your computer's web browser.

eReaders and other devices

To read on e-ink devices like the Sony eReader or Barnes & Noble Nook, you'll need to download a file and transfer it to your device. Please follow the detailed Help center instructions to transfer the files to supported eReaders.
A New York Times Bestseller

An audacious, irreverent investigation of human behavior—and a first look at a revolution in the making
 
Our personal data has been used to spy on us, hire and fire us, and sell us stuff we don’t need. In Dataclysm, Christian Rudder uses it to show us who we truly are.
 
For centuries, we’ve relied on polling or small-scale lab experiments to study human behavior. Today, a new approach is possible. As we live more of our lives online, researchers can finally observe us directly, in vast numbers, and without filters. Data scientists have become the new demographers.
 
In this daring and original book, Rudder explains how Facebook "likes" can predict, with surprising accuracy, a person’s sexual orientation and even intelligence; how attractive women receive exponentially more interview requests; and why you must have haters to be hot. He charts the rise and fall of America’s most reviled word through Google Search and examines the new dynamics of collaborative rage on Twitter. He shows how people express themselves, both privately and publicly. What is the least Asian thing you can say? Do people bathe more in Vermont or New Jersey? What do black women think about Simon & Garfunkel? (Hint: they don’t think about Simon & Garfunkel.) Rudder also traces human migration over time, showing how groups of people move from certain small towns to the same big cities across the globe. And he grapples with the challenge of maintaining privacy in a world where these explorations are possible.
 
Visually arresting and full of wit and insight, Dataclysm is a new way of seeing ourselves—a brilliant alchemy, in which math is made human and numbers become the narrative of our time.


From the Hardcover edition.
With more than 200 practical recipes, this book helps you perform data analysis with R quickly and efficiently. The R language provides everything you need to do statistical work, but its structure can be difficult to master. This collection of concise, task-oriented recipes makes you productive with R immediately, with solutions ranging from basic tasks to input and output, general statistics, graphics, and linear regression.

Each recipe addresses a specific problem, with a discussion that explains the solution and offers insight into how it works. If you’re a beginner, R Cookbook will help get you started. If you’re an experienced data programmer, it will jog your memory and expand your horizons. You’ll get the job done faster and learn more about R in the process.

Create vectors, handle variables, and perform other basic functionsInput and output dataTackle data structures such as matrices, lists, factors, and data framesWork with probability, probability distributions, and random variablesCalculate statistics and confidence intervals, and perform statistical testsCreate a variety of graphic displaysBuild statistical models with linear regressions and analysis of variance (ANOVA)Explore advanced statistical techniques, such as finding clusters in your data

"Wonderfully readable, R Cookbook serves not only as a solutions manual of sorts, but as a truly enjoyable way to explore the R language—one practical example at a time."—Jeffrey Ryan, software consultant and R package author

©2018 GoogleSite Terms of ServicePrivacyDevelopersArtistsAbout Google|Location: United StatesLanguage: English (United States)
By purchasing this item, you are transacting with Google Payments and agreeing to the Google Payments Terms of Service and Privacy Notice.