ModelingComplexSystems
2020-01-12

 

 

Table: Biosystems Resources v1.12

 
 

FIELD

SUBJECT

TOPIC

PRINCPAL RESOURCES

SUPPORTING RESOURCES

MATHEMATICS MATHEMATICS Overview

Steven Strogatz

The Joy of x:

A guided tour of math, from one to infinity

Keith Devlin

Mathematics:

The new golden age

       

W. W. Sawyer

Prelude to Mathematics

       

G. H. Hardy

A Mathematician's Apology

       

Sarah Flannery

In Code:

A mathematical journey

     

Jeremy Kun
A Programmer's Introduction to Mathematics

ch 01: Like Programming, Mathematics has a Culture

ch 07: The Many Subcultures of Mathematics

 
     

(WEB)

https://arxiv.org/pdf/math/0503081.pdf

William P. Thurston

Mathematical Education

 
     

(WEB)

https://arxiv.org/pdf/math/9404236.pdf

William P. Thurston

On Proof and Progress in Mathematics

 
    Review

John Vince

Mathematics for Computer Graphics

 

 

 

 

Logic

Patrick J. Hurley

Logic: A Concise Introduction, 12th ed.

 

     

Daniel J. Velleman

How to Prove It:

A structured approach

ch 01: Sential Logic

ch 02: Quantificational Logic

ch 03: Proofs

ch 06: Mathematical Induction

Antonella Cupillari

The Nuts and Bolts of Proofs

 

 

Analysis

Lara Alcock

How to Study as a Mathematics Major

Keith Devlin

Introduction to Mathematical Thinking

     

Laura Alcock

How to Think About Analysis

 
    Real Analysis

Stephen Abbott

Understanding Analysis, 2nd ed.

 
     

Terence Tao

Analysis I, 3rd ed.

Terence Tao

Analysis II, 3rd ed.

       

Edmund Landau

Foundations of Analysis

     

Jeremy Kun
A Programmer's Introduction to Mathematics

ch 02: Polynomials

ch 03: On Pace and Patience

 

 

 

Linear Algebra

Philip N. Klein

Coding the Matrix:

Linear Algebra through computer science ppplications, 1st ed.

Stephen Friedberg

Introduction to Linear Algebra with Applications, 1st ed.

     

 

Seymour Lipschutz

Schaum's Outline Series

Theory and Problems of Linear Algebra

     

Jeremy Kun
A Programmer's Introduction to Mathematics

ch 09: On Types and Tail Calls

ch 10: Linear Algebra

ch 11: Live and Learn Linear Algebra
ch 12: Eignevalues and Eigenvectors

 

 

 

Discrete

Mathematics

Bernard Kolman

Discrete Mathematical Structures, 4th ed.

Seymour Lipschutz

Schaum's Outline Series

Discrete Mathematics, 2nd ed.

     

(DVD)

The Great Courses

Arthur T. Benjamin

Discrete Mathematics

Arthur T. Benjamin

The Great Courses: Course Guidebook:

Discrete Mathematics

       

Allan M. Stavely

Programming and Mathematical Thinking:

A gentle introduction to discrete math featuring Python

 

 

 

 

Amit Saha

Doing Math with Python:

Use programming to explore algebra, statistics, calculus, and more

(ch5: Playing with Sets and Probability)

     

Jeremy Kun
A Programmer's Introduction to Mathematics
ch 04: Sets

Charles Pinter

A Book of Set Theory

    Calculus

Michael Spivak

Calculus, 4th ed.

James Stewart

Calculus:

Early transcendentals, 8th ed.

     

Steven Strogatz

Infinite Powers:

How calculus reveals the secrets of the universe

 
      Jeremy Kun
A Programmer's Introduction to Mathematics
ch 08: Calculus with One Variable
 

 

 

 

William E. Boyce

Elementary Differential Equations and Boundary Value Problems, 9th ed.

Brian R. Hunt

Differential Equations with MATLAB, 2nd ed.

 

 

 

 

Staff of Research and Education Association

Advanced methods for solving differential equations

    Advanced Calculus

Mary L. Boas

Mathematical Methods in the Physical Sciences, 3rd ed.

Francis B. Hildebrand

Advanced calculus for applications

      Jeremy Kun
A Programmer's Introduction to Mathematics
ch 14: Multivariable Calculus and Optimization
 
     

Daniel Fleisch

A Student's Guide to Vectors and Tensors

 
     

H. M. Schey

div grad curl and all that:

An informal text on vector calculus

 
     

John Vince

Vector Analysis for Computer Graphics

 

 

 

 

John Vince

Quaternions for Computer Graphics

 

    Functional Analysis

John M. H. Olmstead

Real Variables:

An Introduction to the Theory of Functions

Francis J. Flanigan

Calculus Two: Linear and Nonlinear Functions

     

Daniel G. Luenberger

Optimization by Vector Space Methods

ch 01-07

 
     

Philippe G. Ciarlet

Linear and Nonlinear Functional Analysis with Applications

Gerald Jay Sussman

Functional Differential Geometry

(utilizing the Scheme programming language)

 

 

Probability

Joseph K. Blitzstein

Introduction to Probability

Murray R. Spiegel

Schaum's Outline Series

Theory and Problems of Probability and Statistics

 

 

 

Richard T. Cox

The Algebra of Probable Inference

 

     

Philippe Flajolet, Robert Sedgewick

Analytic Combinatorics

 

 

 

Statistics

Sam Kash Kachigan

Multivariate Statistical Analysis:

A conceptual introduction

Lyman Ott

An Introduction to Statistical Methods and Data Analysis

 

 

 

 

Murray R. Spiegel

Schaum's Outline Series

Theory and Problems of Probability and Statistics

 

 

 

John K. Kruschke

Doing Bayesian Data Analysis:

A tutorial with R and BUGS

James V. Stone

Bayes' Rule

A tutorial introduction to Bayesian Analysis

 

 

 

Norman Matloff

The Art of R Programming:

A tour of statistical software design

 

 

 

 

Judea Pearl

Causality:

Models, Reasoning and Inference, 2nd ed.

Judea Pearl

Causal inference in Statistics: A Primer

 

 

 

Richard T. Cox

The Algebra of Probable Inference

 

 

 

Complex Analysis

Paul J. Nahin

An Imaginary Tale:

The story of √-1

 

     

Paul J. Nahin

Dr. Euler's Fabulous Formula

 

 

 

 

Gino Moretti

Functions of a Complex Variable

Murray R. Spiegel

Schaum's Outline Series

Theory and Problems of Complex Variables:

with an introduction to conformal mapping and its applications

     

John Vince

Quaternions for Computer Graphics

 

 

 

Numerical Analysis and Methods

Timothy Sauer

Numerical Analysis 3rd ed.

Steven C. Chapra

Numerical Methods for Engineers, 7th ed.

 

 

 

 

CREI

Numerical Analysis I, 1717

 

 

 

 

CREI

Numerical Analysis II, 1718

 

 

 

 

F.B. Hildebrand

Introduction to Numerical Analysis

 

 

 

Ronald Mak

The Java Programmer's Guide to Numerical Computing

Bruce E. Shapiro

Scientific Computation:

Python Hacking for Math Junkies, 2nd ed., Rev

 

 

 

Mark Newman

Computational Physics

 

     

Rubin H. Landau

Computational Physics:

Problem solving with Python

 

 

 

Graph Theory

Arthur Benjamin

The Fascinating World of Graph Theory

 

     

Frank Harary

Graph Theory

 
      Jeremy Kun
A Programmer's Introduction to Mathematics
ch 06: Graphs
 

 

 

Topology

Joseph O'Rourke

How to Fold It:

The Mathematics of linkages, origami, and polyhedra

(DVD)

PBS: NOVA

The Origami Revolution

 

 

 

 

Dennis Roseman

Elementary Topology

 

    Abstract Algebra Jeremy Kun
A Programmer's Introduction to Mathematics
ch 16: Groups
 
     

David S. Dummit

Abstract Algebra, 3rd ed.

 
    Fractal Geometry

Benoit Mandelbrot

The Fractal Geometry of Nature

 
     

Michael Barnsley

Fractals Everywhere

 
     

Roger T. Stevens

Fractal Programming in C

 
    Chaos

Robert L. Devaney (ed.)

Chaos and Fractals:

The mathematics behind the computer graphics

John Briggs

Fractals:

The patterns of chaos

       

James Gleick

Chaos:

Making of a New Science

 

 

 

 

 

NATURAL SCIENCES PHYSICS Overview

Kenneth W. Ford

Basic Physics

ch 01: The scientist's view of the world

ch 02: Elementary Particles

ch 03: The large and the small

ch 04: Conservation laws

ch 05: Mathematics in science

ch 06: Vectors

ch 07: Units, functions, and graphs

ch 28: The progress of science

Leonard Susskind

The Theoretical Minimum:

What you need to know to start doing physics

ch 01: The nature of classical physics

       

James Gleick

Isaac Newton

       

Richard Feynman

The Character of Physical Law

       

Carlo Rovelli

Seven Brief Lessons On Physics

       

Andrew Thomas

Hidden In Plain Sight 3:

The secret of time

    Mechanics

Kenneth W. Ford

Basic Physics

ch 08: The laws of motion

ch 09: Momentum

ch 10: Angular momentum

ch 11: Energy

ch 12: Universal gravitation and the evolution of mechanics

 

 

 

 

John R. Taylor

Classical Mechanics

Michael Spivak

Physics for Mathematicians

Mechanics I

     

 

 

Dare  A. Wells

Schaum's Outline Series

Theory and Problems of Lagrangian Dynamics

 

 

 

Anders Malthe-Sorenson

Elementary Mechanics Using Python:

A modern course combining analytical and numerical techniques

Colin Pask

Magnificent Principia:

Exploring Isaac Newton's Masterpiece

    Fluid Mechanics

Yunus Cengal

Fluid Mechanics:

Fundamentals and applications. 4th ed.

 
     

Frank White

Fluid Mechanics, 8th ed.

Rutherford Aris

Vecrors, Tensors, and the Basic Equations of Fluid Mechanics

     

David A. Rubenstein

Biolfluid Mechanics

 
   

Harmonic Motion

Walter Fox Smith

Waves and Oscillations:

A prelude to quantum mechanics

 
     

Steven Strogatz

Sync:

The emerging science of spontaneous order

 
    Electromagnetics

Kenneth W. Ford

Basic Physics

ch 15: Electrostatics and magnetostatics

ch 16: Electromagnetism

ch 17: Applications of electromagnetism

ch 18: Electromagnetic radiation and wave phenomena

 

 

 

 

David J. Griffiths

Introduction to Electrodynamics, 4th ed.

Dale Corson

Introduction to Electromagnetic Fields and Waves

 

 

 

 

Daniel Fleisch

A Student's Guide to Maxwell's Equations

    Thermodynamics

Kenneth W. Ford

Basic Physics

ch 13: Temperaure, heat, and the kinetic theory

ch 14: Entropy and the second lae of thermodynamics

 

 

 

 

M. Scott Shell

Thermodynamics and Statistical Mechanics:

An Integrated Approach

Peter Atkins

The Laws of Thermodynamics:

A Very Short Introduction

 

 

 

 

M. M. Abbott

Schaum's Outline Series

Thermodynamics

 

 

 

Ken A. Dill

Molecular Driving Forces:

Statistical Thermodynamics in Biology,

Chemistry, Physics, and Nanoscience, 2nd ed.

 

   

Modern Classical Physics

 

Kip S. Thorn

Modern Classical Physics:

Optics, Fluids, Plasmas, Elasticity, amd Statistical Physics

 
    Quantum Mechanics

Kenneth W. Ford

Basic Physics

ch 23: The key ideas of quantum mechanics

ch 24: Atoms

ch 25: Nuclei

ch 26: Particles and interactions

ch 27: The submicroscopic frontier

Kenneth W. Ford

The Quantum World:

Quantum Physics for Everyone

     

Walter Fox Smith

Waves and Oscillations:

A prelude to quantum mechanics

 

 

 

 

David J. Griffiths

Introduction to Quantum Mechanics, 2nd ed.

 

 

 

 

John R. Taylor

Modern Physics for Scientists and Engineers, 2nd. ed.

 

   

Computational Physics

Mark Newman

Computational Physics

 
     

Rubin H. Landau

Computational Physics:

Problem solving with Python

 

 

 

Fantasy

Roger Penrose

Fashion, Faith and Fantasy in the New Physics of the Universe

 

 

 

 

Sabine Hossenfelder

Lost in Math:

How beauty leads physics astray

 

 

 

 

John G. Cramer

The Quantum Handshake:

Entanglement, nonlocality, and transactions

 

 

 

 

George Greenstein

Quantum Strangeness:

Wrestling with Bell's theorem and the ultimate nature of reality

 

     

Paul Halpern

The Quantum Labyrinth:

How Richard Feynman and John Wheeler revolutionized time and reality

 
     

Sean Carroll

Something Deeply Hiddes:

Quantum worlds and the emergence of spacetime

 
         

 

INFORMATION

Theory

James V. Stone

Information Theory:

A tutorial introduction

Luciano Floridi

Information:

A very short introduction

 

 

Science

David G. Luenberger

Information Science

 

 

 

Entropy

Richard T. Cox

The Algebra of Probable Inference

 

 

 

 

Acquisition

Thomas R. Gruber

The Acquisition of Strategic Knowledge

 

   

Organization

Robert J. Glushko

The Discipline of Organizing

 
   

 

Robert Arp

Building Ontologies with Basic Formal Ontology

 
   

 

Graph-based Knowledge Representation:

Computational foundations of conceptual graphs

 
   

Management

Ofer Bergman

The Science of Managing our Digital Stuff

 
     

Robert J. Glushko

Document Engineering

 
         

 

CHEMISTRY

Inorganic Chemistry

Peter Atlins

Chemical Principles:

The Quest for Insight, 5th ed.

Peter Atkins

Chemistry:

A Very Short Introduction

 

 

 

 

CD

Loretta Jones

Bridging to the Lab:

Media Connecting Chemistry Concepts with Practice

 

 

 

DVD: The Great Courses

Ron B. Davis

Chemistry and Our Universe

How it All Works:

Ron B. Davis

The Great Courses: Course Guidebook

Chemistry and Our Universe:

How it All Works:

 

 

 

 

Adrian Dingle

The Elements:

A tour of the periodic table

 

 

 

Michael J. Pilling

Reaction Kinetics

 

 

 

Organic Chemistry

William Brown

Introduction to Organic Chemistry, 4th ed.

Graham Patrick

Organic Chemistry

A Very Short Introduction

 

 

 

DVD: The Great Courses

Ron B. Davis Jr.

Foundations of Organic Chemistry:

Ron B. Davis Jr.

The Great Courses: Course Guidebook

Foundations of Organic Chemistry:

 

 

Biochemistry

Reginald H. Garrett

Biochemistry, 6th ed.

Lubert Stryer

Biochemistry, 4th ed.

 

 

Physical Chemistry

Peter Atkins

Physical Chemistry:

Thermodynamics, Structure, and Change, 10th ed.

Peter Atkins

Physical Chemistry:

A Very Short Introduction

 

 

 

 

Ken A. Dill

Molecular Driving Forces:

Statistical Thermodynamics in Biology,

Chemistry, Physics, and Nanoscience, 2nd ed.

 

 

 

 

Quantum Chemistry

Ira N. Levine

Quantum Chemistry, 7th ed.

 

 

 

 

 

 

 

BIOLOGY

General Biology

Jane B. Reece

Campbell Biology, 10th ed.

 

 

 

 

(DVD)

The Great Courses

Stephen Nowicki

Biology: The Science of Life

Stephen Nowicki

The Great Courses: Course Guidebook

Biology: The Science of Life

    Health    

 

 

Health: Cancer

Robert A. Weinberg

The Biology of Cancer, 2nd ed.

Lauren Pecorino

Molecular Biology of Cancer:

Mechanisms, targets, and Therapeutics

 

 

 

Emmanuel Barillot

Computational Systems Biology of Cancer

 

 

 

 

Vittorio Cristini

Multiscale Modeling of Cancer:

An integrated experimental and mathematical modeling approach

 

 

 

 

Faiz M. Kahn

The Physics of Radiation Therapy, 5th ed.

Eric J. Hall

Radiobiology for the Radiologist, 7th ed.

 

 

 

Rene Chee

Curing Cancer with Immunotherapy

 

 

 

Health: Aging

Roger B. McDonald

Biology of Aging

 

 

 

 

Health: Immunology

Judith Owen

Kuby Immunology, 7th ed.

 

 

 

 

Charles Graeber

The Breakthrough:

Immunotherapy and the race to cure cancer.

 

 

 

 

Rene Chee

Curing Cancer with Immunotherapy

 

 

 

Health: Nutrition

Sareen S. Gropper

Advanced Nutrition and Human Metabolism

 

 

 

Anatomy & Physiology

Frederic H. Martini

Fundamentals of Anatomy & Physiology, 9th ed.

Frederick H. Martini

Martini's Atlas of the Human Body

 

 

 

 

Gerard J. Tortora

Principles of Anatomy  & Physiology, 14th ed.

 

 

 

(DVD)

The Great Courses

Anthony A. Goodman

Understanding the Human Body:

An introduction to anatomy and physiology

Anthony A. Goodman

The Great Courses: Course Guidebook

Understanding the Human Body:

An introduction to anatomy and physiology

 

 

Plant Biology

Peter H. Raven

Biology of Plants

Daniel Chamovitz

What a Plant Knows:

A field guide to the senses

 

 

Microbiology

Gerard J. Tortora

Microbiology: An Introduction

 

 

 

Molecular Biology

David P. Clark

Molecular Biology

Bruce Alberts

Molecular Biology of the Cell, 6th ed.

 

 

 

John Kuriyan

The Molecules of Life:

Physical and Chemical Principles

 

 

 

 

Peter M. Hoffmann

Life's Ratchet:

How molecular machines extract order from chaos

 

 

 

 

David S. Goodsell

The Machinery of Life

 

 

 

 

Sorin Draghici

Statistics and Data analysis for Microarrays

Using R and Bioconductor, 2nd ed.

 

 

 

 

WEB

Fundamentals of Biology

MIT, Eric Lander et al.

https://ocw.mit.edu/courses/biology/7-01sc-fundamentals-of-biology-fall-2011/index.htm

 

 

 

Information

Paul Davies

The Demon in the Machine:

How hidden webs of information are solving the mystery of life

 

 

 

 

Sara Imari Walker

From Matter to Life:

Information and Causality

 

 

 

Genetics

Benjamin A. Pierce

Genetics: A Conceptual Approach, 4th ed.

Anthony J. F. Griffiths, David T. Suzuki

An Introduction to Genetic Analysis, 5th ed.

 

 

 

 

Megan Smolenyak

Trace Your Roots with DNA:

Using Genetic Tests to Explore Your Family Tree

 

 

Developmental Biology

Scott F. Gilbert

Developmental Biology, 11th ed.

 

 

 

Biotechnology

David P. Clark

Biotechnology, 2nd ed.

 

 

 

Bioinformatics

Arthur M. Lesk

Introduction to Bioinformatics, 4th ed.

 

 

 

Evolution

John H. Holland

Adaptation in Natural and Artificial Systems:

An introductory analysis with applications to biology, control, and artificial intelligence

 

 

 

 

Bruce Wallace

Adaptation

 

 

 

 

Verne Grant

The Origin of Adaptations

Charles Darwin, James t. Costa, annotator

On the Origin of Species, 1st ed., Annotated

 

 

 

Andreas Wagner

The Origins of Evolutionary Innovations:

A Theory of Transformative Change in Living Systems

Andrea Wagner

Arrival of the Fittest:

Solving Evolution's Greatest Puzzle

 

 

 

Richard Dawkins

The Selfish Gene

Martin A. Nowak

Super Cooperators:

Altruism, evolution, and why we need each other to Succeed

 

 

 

David Quammen

The Tangled Tree:

A Radical New History of Life

 

 

 

Epigenetics

Richard Dawkins

The Extended Phenotype

Simon Conway Morris

The Runes of Evolution:

How the universe Became self-aware

 

 

 

Nessa Carey

The Epigenetics Revolution:

How modern biology is rewriting our understanding of genetics, disease, and inheritance

Sean B. Carroll

Endless Forms Most Beautiful:

The new science of Evo Devo

 

 

 

Alan Jasanoff

The Biological Mind:

How brain, body, and environment collaborate to make us who we are

 

 

 

 

 

James L. Gould, ed.

Life at the Edge

Jack Horner

How to Build a Dinosaur:

Extinction doesn't have to be forever

 

 

 

Daniel C. Dennett

From Bacteria to Back and Back:

The Evolution of Minds

Steven Pinker

How the Mind Works

    Behavior

Robert M. Sapolsky

Behave:

The Biology of Humans at Our Best and Worst

 

 

 

Causality

Sari Imari Walker

From Matter to Life:

Information and Causality

 

 

 

 

Manfred Eigen

Steps Towards Life:

A perspective on evolution

 

 

 

Cognition

Steven Pinker

How the Mind Works

 

 

 

 

Daniel C. Dennett

From Bacteria to Back and Back:

The Evolution of Minds

 

 

 

 

Adam Gazzaley

The Distracted Mind:

Ancient brains in a high tech world

 

 

 

Biophysics

Thomas M. Nordlund

An Introduction to Biophysics:

Quantitative Understanding of Biosystems

 

 

 

 

Philip Nelson

Biological Physics:

Energy, Information, Life

David A. Rubenstein
Biofluid Mechanics:
An Introduction to fluid mechanics, macrocirculation, and microcirculation, 2nd ed.

 

 

 

Rob Phillips

Physical Biology of the Cell, 2nd ed.

Ron Milo; Rob Phillips

Cell Biology by the Numbers

 

 

 

Donald T. Haynie

Biological Thermodynamics

 

 

 

 

Ken A. Dill

Molecular Driving Forces:

Statistical Thermodynamics in Biology,

Chemistry, Physics, and Nanoscience, 2nd ed.

 

      Benoit B Mandelbrot
The Fracal Geometry of Nature
 

 

 

Computational

Biology

Michael S. Waterman

Introduction to Computational Biology:

Maps, sequences, and genomes

 

 

 

 

Martin A. Nowak

Evolutionary Dynamics:

Exploring the Equations of Life

Charles S. Cockell

The Equations of Life:

How physics shapes evolution

 

 

 

Boris Ja. Kogan

Introduction to Computational Cardiology:

Mathematical Modeling and Computer Simulation

Sachse, Frank B.

Computational Cardiology

Modeling of Anatomy, Electrophysiology, and Mechanics

 

 

 

Philip Nelson

Physical Models of Living Systems

 

 

 

Systems Biology

Eberhard O. Voit

A First Course in Systems Biology

Eberhard O.  Voit

The Inner Workings of Life:

Vignettes in Systems Biology

 

 

 

Andreas Kremling

Systems Biology:

Mathematical Modeling and Model Analysis

 

 

 

 

Brian P. Ingalls

Mathematical Modeling in Systems Biology

 

 

 

 

Joseph DiStefano III

Dynamic Systems Biology Modeling and Simulation

 

 

 

Gene Regulatory Networks

Hamid Bolouri

Computational Modeling of Gene Regulatory Networks:

A Primer

 

 

 

 

Uri Alon

An Introduction to Systems Biology:

Design Principles of Biological Circuits

 

 

 

Feedback Control

Carlo Cosentino

Feedback Control in Systems Biology

Pablo A. Igleslas, ed.

Control Theory and Systems Biology

 

 

 

 

Sean B. Carroll

The Serengeti Rules:

The quest to discover how life works and why it matters

 

 

 

 

Fred S. Grodins

Respiratory Function of the lung and its control

Fred S. Grodins

Control Theory and Biological Systems

 

 

Quantum Biology

Masoud Mohseni

Quantum Effects in Biology

Johnjoe McFadden

Life on the Edge:

The Coming Age of Quantum Biology

 

 

 

 

 

ENGINEERING

COMPUTER

SCIENCE

Java Programming Language

Cay S. Horstmann

Core Java SE 9 for the Impatient. 2nd ed.

Cay S. Horstmann

Core Java:

Volume I — Fundamentals, 11th ed.

 

 

 

 

Cay S. Horstman

Core Java:

Volume II —  Advanced Features, 11th ed.

     

 

Ken Arnold

The Java Programming Language, 4th ed.

     

Herbert Schildt

Java:

The Complete Reference, 11th ed.

 
      (MEAP)
NIcolai Parlog
The Java Module System

 

 

 

Programming in Java

Robert Sedgewick
Computer Science:
An interdisciplinary approach

ch 01: Elements of Programming

ch 02: Functions and Modules

ch 03: Object Oriented Programming

ch 04: Algorithms and Data Structures

 

     

(WEB)

http://www.informit.com/store/computer-science-video-lectures-20-part-lecture-series-9780134493831

Robert Sedgewick
Computer Science:
An interdisciplinary approach

lec 01-10

 

 

 

Python Programming Language

Charles Russell Severance

Python for Everybody:

Exploring Data in Python 3

Mark Lutz

Python Pocket Reference:

Python in your pocket

 

 

 

Jesse M. Kinder

A Student's Guide to Python for Physical Modeling

 

    Programming in Python

Robert Sedgewick

Introduction to Programming in Python:

An interdisciplinary approach

 
    Introduction to Computer Science

Robert Sedgewick
Computer Science:
An interdisciplinary approach
ch 05: Theory of Computing
ch 06: A Computing Machine
ch 07: Building a Computing Device

 

     

(WEB)

http://www.informit.com/store/computer-science-video-lectures-20-part-lecture-series-9780134493831

Robert Sedgewick
Computer Science:
An interdisciplinary approach

lec 11-20

 
      Chris Bernhardt
Turing's Vision: The Birth of Computer Science
George Dyson
Turing's Cathedral:
The origins of the digital universe
     

Jeremy Kun
A Programmer's Introduction to Mathematics

ch 05: Variable Names, Overloading, and Your Brain

ch 13: Rigor and formality

ch 15: The Argument for Big-O Notation

 
    Algorithms

Robert Sedgewick

Algorithms, 4th ed.

Robert Sedgewick

Algorithms in Java, 3rd ed.

Parts 1-4:

Fundamentals, Data Structures, Sorting, Searching

    Analysis of Algorithms Robert Sedgewick, Philippe Flajolet
An Introduction to the Analysis of Algorithms, 2nd ed.
 
      (WEB)
Robert Sedgewick
An Introduction to the Analysis of Algorithms, 6 Lectures
https://aofa.cs.princeton.edu/online/index.cgi
 

 

 

MATLAB

(WEB)

https://www.mathworks.com/help/pdf_doc/matlab/index.html?s_cid=doc_ftr

The MathWorks

PDF Documentation for MATLAB:

Primer

Desktop tools and development environment

Graphics

Java and Python API reference

MAT-File format

 

 

 

Graphics: JavaFX 8 Programming

 

Kishori Sharan

Learn JavaFX 8:

Building User Experience and Interfaces with Java  8

Hendrik Ebbers

Mastering JavaFX 8 Controls:

Create custom JavaFX Controls for Cross-Platform Applications

 

 

 

Gail Anderson

JavaFX:

Rich Client Programming on the NetBeans Platform

 

 

 

Graphics: Python

Harrison Kinsley

Beginning Python Games Development:

With PyGame

 

 

 

Graphics: MATLAB

MATLAB Graphics, op. cit.

 

    UML

Russ Miles
Learning UML 2.0
ch 04: Modeling a Systems's Logical Structure:
Introducing classes and class diagrams
ch 05: Modeling a System's Logical Structure:
Advanced Class Diagrams
ch 06: Bringing Your Classes to Life:
Object Diagrams

 

 

 

Advanced Java

Programming Language

Raoul-Gabriel Urma

Java 8 in Action:

Lambdas, streams, and functional-style programming

Maurice Naftalin

Mastering Lambdas:

Java programming in a multicore world

 

 

 

Cay S. Horstmann

Core Java:

Volume II — Advanced Features, 11th ed.

 

 

 

Database Programming

Robin Nixon

Learning PHP, MySQL. & JavaScript

Ben Forta

MySQL:

Crash Course

 

 

 

 

Mark Matthews

MySQL and Java Developer's Guide

 

 

Graph Algorithms

Robert Sedgewick

Algorithms in Java, 3rd ed.

Parts 5: Graph Algorithms

Giuseppe Di Battista

Graph Drawing:

Algorithms for the Visualization of Graphs

 

 

Operating Systems

Andrew S. Tanenbaum

Operating Systems:

Design and development, 3rd ed.

Brian Ward

How Linux Works:

What every superuser should know, 2nd ed.

 

 

 

 

Rickford Grant

Ubuntu for Non-Geeks:

A pain free, get things done guide.

 

 

Windows OS Internals and Utilities

Mark Russinovich

Windows Internals, 7th ed.

Part 1:

System Architecture, processes, threads, memory management, and more

Brian Knittel

Windows 10 In Depth

 

 

 

Brian Knittel

Windows 7 Guide to Scripting, Automation,

and Command Line Tools

 

 

 

 

Mark Russinovich

Windows Internals, 7th ed.

Part 2

 

 

 

Security

Michael T. Goodrich

Introduction to Computer Security

Sarah Flannery

In Code:

A mathematical journey

ch 06: The Arithmetic of Cryptography

ap A: "Cryptography — A New Algorithm Versus the RSA"

 

 

Machine Intelligence

Franҫois Chollet

Deep Learning with Pyton

 

 

 

 

Ian Goodfellow

Deep Learning

Tom M. Mitchell

Machine Learning

 

 

 

Alan M.F. Souza

Neural Network Programming with Java, 2nd ed.

 

 

 

 

David E. Goldberg

Genetic Algorithms:

In search, optimization & machine learning

 

 

 

 

Judea Pearl

Probabilistic Reasoning in Intelligent Systems

 

 

 

Pattern Recognition

Christopher M. Bishop

Pattern Recognition and Machine Learning

Julius T. Tau, ed.

Advances in Information Systems Science

 

 

Animation

Rick Parent

Computer Animation:

Algorithms & Techniques, 3rd ed.

Eric Lengyel

Mathematics for 3D Game Programming and Computer Graphics, 3rd ed.

 

 

 

John Vince

Quaternions for Computer Graphics

John Vince

Vector Analysis for Computer Graphics

 

 

Information Storage and Retrieval

Christopher D. Manning

Introduction to Information Retrieval

Charles Russell Severence

Python for Everybody:

Exploring Data in Python 3

 

 

 

Stefan Büttcher

Information Retrieval

Robert R. Korfhage

Information Storage and Retrieval

 

 

Website Development

David Sawyer McFarland

Dreamweaver CC:

The missing manual, 2nd ed.

 

 

 

 

Jim Maivald

Adobe Dreamweaver CC: Classroom in a Book, 2019 Release

 

 

 

 

Robin Nixon

Learning PHP, MySQL & JavaScript with JQUERY, CSS & HTML5

 

 

 

 

Elizabeth Castro

HTML5 AND CSS3, 7th ed.

 

 

 

Network Communications

John Rhoton

Programmer's Guide to Internet Mail

Lawrence Hughes

Internet e-mail:

protocols, standards, and implementation

 

 

 

 

Peer Heinlein

The Book of IMAP:

Building a mail server with Courier and Cyrus

 

 

 

Leonard Rosenthol

Developing with PDF:

Dive into the Portable Document format

 

 

 

 

 

 

 

 

CONTROL SYSTEMS

ENGINERING

Signals and Systems

Luis F. Chaparro

Signals and Systems Using MATLAB

 

 

 

 

CREI

Introduction to Communications, 250-01

 

 

 

Control Systems

Norman S. Nise

Control Systems Engineering, 7th ed.

Richard C. Dorf

Modern Control Systems, 2nd ed.

 

 

Dynamical Systems

David G. Luenberger

Introduction to Dynamic Systems:

Theories, Models, & Applications

 

 

 

Nonlinear Systems

W. J. Cunningham

Introduction to Nonlinear Analysis

 

 

 

 

Arturo Buscarino

Essentials of Nonlinear Circuit Dynamics with MATLAB and Laboratory Experiments

 

 

 

 

George J. Thaler

Analysis and Design of Nonlinear Feedback Control Systems

 

 

 

 

Chihiro Hayashi

Nonlinear Oscillations in Physical Systems

 

 

 

 

 

 

 

ELECTRICAL AND ELECTRONIC ENGINEERING

Linear Circuit Theory

Steven T. Karris

Circuit Analysis I:

with MATLAB Applications

Jiri Vlach

Linear Circuit Theory

 

 

 

 

Peter H. O'N. Roe Networks and Systems

 

 

 

 

CREI

Network Analysis, 1715

 

 

 

Jacob Millman

Integrated Electronics:

Analog and Digital Circuits and Systems

 

 

 

 

Steven T. Karris

Circuit Analysis II:

with MATLAB Computing and Simulink/SimPowerSystems Modeling

CREI

Network Synthesis, 1716

 

 

Nonlinear Circuit Theory

Arturo Buscarino

Essentials of Nonlinear Circuit Dynamics with MATLAB and Laboratory Experiments

 

 

 

 

CREI

Nonlinear Electrical Networks I, 1719

 

 

 

 

CREI

Nonlinear Electrical Networks II, 1720

 

 

 

 

 

 

 

OPERATIONS RESEARCH

Operations Research

Frederick S. Hillier

Operations Research

 

 

 

Optimization

A. O. Converse

Optimization

 

 

 

 

Gerald E. Thompson

Linear Programming

 

 

 

Queuing Theory

Edward D. Lazowska

Quantitative System Performance:

Computer System Analysis Using Queueing Network Models

 

 

 

Decision Theory

Charles A. Holloway

Decision Making Under Uncertainty:

Models and Choices

 

 

 

 

 

 

 

SYSTEMS

ENGINEERING

 

Networks

Mark Newman

Networks: An Introduction

Peter H. O'N. Roe Networks and Systems

 

 

 

Edward D. Lazowska

Quantitative System Performance:

Computer system analysis using queueing network models

 

 

 

 

Daphne Koller

Probabilistic Graphical Models:

Principles and Techniques

(ch1-2)

 

 

 

 

Joseph Loscalzo

Network Medicine:

Complex systems in human disease and therapeutics

 

 

 

Discrete Event Systems

Christos G. Cassandras

Discrete Event Systems:

Modeling and Performance Analysis

Edward D. Lazowska

Quantitative System Performance:

Computer System Analysis Using Queueing Network Models

 

 

Complex Systems

Claudius Gros

Complex and Adaptive Dynamical Systems:

A Primer

 

 

 

 

Hiroki Sayama

Introduction to the Modeling and Analysis of Complex Systems

 

 

 

 

Arturo Buscarino

Essentials of Nonlinear Circuit Dynamics with MATLAB and Laboratory Experiments

 

 

 

Adaptive Systems

Daphne Koller

Probabilistic Graphical Models:

Principles and Techniques

WEB

Daphne Koller

https://www.coursera.org/specializations/probabilistic-graphical-models

 

 

 

 

Julius T. Tou, ed.

Advances in Information Systems Science

 

 

 

Judea Pearl

Probabilistic Reasoning in Intelligent Systems:

Networks of Plausible Inference

Richard T. Cox

The Algebra of Probable Inference

 

 

 

John H. Holland

Signals and Boundaries:

Building Blocks for Complex Adaptive Systems

 

 

 

 

John H. Holland

Adaptation in Natural and Artificial Systems

 

 

 

Mathematical Modeling

Frank R. Giordano

A First Course in Mathematical Modeling, 5th ed.

Christof Eck

Mathematical Modeling

also

Mathematische Modellierung (Deutsch)

 

 

 

Jesse M. Kinder

A Student's Guide to Python for Physical Modeling

 

 

 

 

Edward Beltrami

Mathematics for Dynamic Modeling

Michael Barnsley
Fractals Everywhere

 

 

 

Sanjoy Mahajan

The Art of Insight in Science and Engineering:

Mastering Complexity

Sanjoy Mahajan

Street-Fighting Mathematics:

The Art of Educated Guessing and Opportunistic Problem Solving

 

 

Qualitative Modeling

Benjamin Kuipers

Qualitative Reasoning:

Modeling and Simulation with Incomplete Knowledge

Albert Rutherford

The Systems Thinker:

Essential thinking skills for solving problems, managing chaos, and creating lasting solutions in a complex world

 

 

Fuzzy Logic

Kazuo Tanaka

An Introduction to Fuzzy Logic for Practical Applications

Daniel McNeill

Fuzzy Logic:

The discovery of a revolutionary computer technology and how it is changing our world

 

 

Finite Element Modeling

Daryl L. Logan

A First Course in the Finite Element Method, 5th ed.

A.J.M. Ferreira

MATLAB codes for Finite Element Analysis

 

 

System Simulation

Narsingh Deo

System Simulation with Digital Computer

M. H. MacDougall

Simulating Computer Systems:

Techniques and tools

 

 

 

 

Scientific and Engineering Software, Inc.

SES/workbench:

Creating Models

 

 

 

 

 

ENVIRONMENTAL

SYSTEMS

ASTROSYSTEMS

Cosmic Rays

Thomas K. Gaisser

Cosmic Rays and Particle Physics, 2nd ed.

Martin A. Pomerantz

Cosmic Rays

(included for historical reasons, mine)

 

 

 

Edmund C. Sutton

Observational Astronomy:

Techniques and Instrumentation

 

 

 

Astronomy

Edward E. Prather

Lecture-Tutorials for Introductory Astronomy

Dinah L. Moché

Astronomy:

A self-teaching guide, 7th ed.

 

 

 

 

John Mosley

Starry Night Companion:

Your guide to understanding the night sky using Starry Night

 

 

 

 

SOFTWARE

Simulation Curriculum

Starry Night Pro

 

 

 

 

 

 

SOLAR SYSTEM

Solar System

Dinah L. Moché

Astronomy:

A self-teaching guide, 7th ed.

 

 

 

Solar Energy

C. Julian Chen

Physics of Solar Energy

John A. Duffie

Solar Energy Thermal Processes

 

 

 

 

 

B. J. Brinkworth

Solar Energy for Man

 

 

 

 

 

 

GEOSYSTEMS

Geosystems

Robert W. Christopherson

Geosystems, 4th ed.

Robert W. Christopherson

Geosystems in the Laboratory, 3rd ed.

 

 

 

Steven M. Stanley

Earth System History, 3rd ed.

Eldridge M. Moores

Tectonics

 

 

Climate Dynamics

John Marshall

Atmosphere, Ocean, and Climate Dynamics:

An Introductory Text

 

 

 

 

 

 

 

BIOSYSTEMS

Biosystems

Thomas M. Nordlund

Quantitative Understanding of Biosystems

An Introduction to Biophysics

 

 

 

 

 

 

 

ECOSYSTEMS

Ecosystems

Kenneth E. F. Watt

Principles of Environmental Science

 

 

 

 

Richard H. W. Bradshaw

Ecosystem Dynamics:

From the past to the future

 

 

 

 

Eugene P. Odum

Fundamentals of Ecology, 3rd ed.

 

 

 

Lyme Disease

Richard S. Ostfeld

Lyme Disease:

The Ecology of a Complex System

 

 

 

Environmental Physics

John L. Monteith

Principals of Environmental Physics:

Plants, Animals, and the Atmosphere, 4th ed.

 

 

 

 

David M. Gates

Biophysical Ecology

 

 

HUMAN ACTIVITIES

Case Studies

Charles A. S. Hall, ed.

Ecosystem Modeling in Theory & Practice:

An introduction with case histories

 

 

 

 

Ahindra Nag, ed.

Biosystems Engineering

 

 

 

 

Herman E. Koenig, ed.

Energy and the Adaptation of Human Settlements

 

 

 

 

Dennis L. Meadows

Dynamics of Growth in a Finite World

 

 

 

 

 

 

SOCIAL SCIENCES

PSYCHOLOGY

Human Nature  

Edward O. Wilson

On Human Nature

 

 

 

 

B. F. Skinner

Science and Human Nature

 

 

 

 

Steven Pinker

Enlightenment Now:

The case for reason, science, humanism, and progress

 

 

 

 

Simon L. Lewis

The Human Planet:

How we created the Anthropocene

 

    Behavior 

Robert M. Sapolsky

Behave:

The Biology of Humans at Our Best and Worst

 

 

 

Intelligence

Daniel Goleman

Emotional Intelligence

Walter Mischell

The Marshmallow Test:

Why self-control is the engine of success

 

 

 

 

Daniel Goleman

Social Intelligence

 

 

 

Creativity

Mihaly Csikszentmihalyi [sic]

Creativity:

Flow and the Psychology of Discovery and Invention

Sidney J. Parnes, ed.

A Source Book for Creative Thinking

 

 

 

 

Sidney J. Parnes

Creative Behavior Guidebook

 

 

 

 

Eugene K. Von Fange

Professional Creativity

 

ECONOMICS

Macroeconomics

Paul A. Samuelson

Economics, 18th ed.

 

 

 

Microeconomics

Richard H. Leftwich

The Price System & Resource Allocation, 6th ed.

 

 

 

 

Anne Steinemann

Microeconomics for Public Decisions, 3rd ed.

 

 

 

Finance

Javier Estrada

Finance in a Nutshell:

A no-nonsense companion to the tool and techniques of finance

 

 

POLICY

Analysis

David L. Weimer

Policy Analysis

 

 

 

 

Deborah Stone

Policy Paradox:

The Art of Political Decision Making, 3rd ed.

 

 

 

Change

Warren G. Bennis, ed.

The Planning of Change

 

 

 

Health Care Delivery Systems

Clayton M. Christensen

The Innovator's Prescription:

A disruptive solution for health care

 

  EDUCATION Philosophy and Practice

David Epstein

Range: Why generalists triumph in a specialized world