ModelingComplexSystems
2020-01-14

 

 

Table: Biosystems Studies Year One v1.5

 
 

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 Applications, 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

         
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

 

INFORMATION

Information Theory

James V. Stone

Information Theory:

A Tutorial Introduction

Luciano Floridi

Information:

A Very Short Introduction

    Acquisition

Thomas R. Gruber

The Acquisition of Strategic Knowledge

 

 

 

 

 

 

 

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

 

 

 

 

 

 

 

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

 

 

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

 

 

 

Molecular Biology

David P. Clark

Molecular Biology

Bruce Alberts

Molecular Biology of the Cell, 6th ed.

 

 

Information

Paul Davies

The Demon in the Machine:

How hidden webs of information are solving the mystery of life

 

 

 

Biotechnology

David P. Clark

Biotechnology, 2nd ed.

 

 

 

Biophysics

Thomas M. Nordlund

An Introduction to Biophysics:

Quantitative Understanding of Biosystems

 

 

 

Systems Biology

Eberhard O. Voit

A First Course in Systems Biology

Eberhard O.  Voit

The Inner Workings of Life:

Vignettes in Systems 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

 

 

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: 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
 

 

 

 

 

 

 

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)

 

 

 

 

 

 

SOCIAL SCIENCES EDUCATION Philosophy and Practice

David Epstein

Range:
Why generalists triumph in a specialized world

 

 
  PSYCHOLOGY Human Nature  

Edward O. Wilson

On Human Nature