Mastering Java through Biology

A bioinformatics project book

• Introduction
  • Who this book is for
  • What's different about this book
    • It's about more than programming
    • It's about scientific computing
    • It's about how to do things

• 1	Computational biology

  • 1.1	Biological applications of computers

  • 1.2	How to use this book

  • 1.3	Java and other languages

    • 1.3.1

      Elements of a program

  • 1.4	The rest of the book

• 2	Your Java environment

  • 2.1	The Java life cycle

  • 2.2

    NetBeans

    • 2.2.1

      Download NetBeans

  • 2.3	Setting up

    • 2.3.1

      Where to put things

    • 2.3.2

      Configuring your ebook reader

  • 2.4	Your first Java program

    • 2.4.1

      Create a new NetBeans project

    • 2.4.2

      The program source

    • 2.4.3

      Run the program

  • 2.5	The context

    • 2.5.1

      From source to runnable program

    • 2.5.2

      Steps in development

  • 2.6	Java versions

  • 2.7	Other Java tools

    • 2.7.1

      Using command windows

    • 2.7.2

      The Java Development Kit

    • 2.7.3

      Other tools

  • 2.8

    Summary

  • 2.9	Projects and exercises

• 3	Java basics

  • 3.1	Chapter preview

  • 3.2	Using the sample code

  • 3.3	A program for numeric data

    • 3.3.1

      The program

  • 3.4

    Types

    • 3.4.1

      Numbers

    • 3.4.2

      Other primitive types

  • 3.5

    Operators

  • 3.6

    Variables

  • 3.7

    Comments

  • 3.8	Declarations

  • 3.9	Initialization

    • 3.9.1

      Assignment

    • 3.9.2

      Combining operations with assignment

    • 3.9.3

      Type conversion

    • 3.9.4

      Running and debugging the program

    • 3.9.5

      Programming style

    • 3.9.6

      Summary

  • 3.10	Arrays and loops

    • 3.10.1

      The program

    • 3.10.2

      Multiple measurements in an array

    • 3.10.3

      For loops

    • 3.10.4

      Summary

  • 3.11	Installing a library

    • 3.11.1

      License agreements

    • 3.11.2

      Installing the Apache commons math library

    • 3.11.3

      Looking at the documentation

  • 3.12	Using classes from a library

    • 3.12.1

      Classes and objects

    • 3.12.2

      Pointing to the class

    • 3.12.3

      Creating a SummaryStatistics object

    • 3.12.4

      Using the SummaryStatistics object

    • 3.12.5

      Summary

  • 3.13	Running your program

    • 3.13.1

      Running inside NetBeans

    • 3.13.2

      Running outside NetBeans

  • 3.14	Projects and exercises

• 4	Simulating a gene
  	Classes and objects

  • 4.1	Chapter preview

  • 4.2	Simulating a single gene

    • 4.2.1

      Advanced note

  • 4.3	Running a program

  • 4.4	Setting up a new program

    • 4.4.1

      File and directory structure

  • 4.5	The main class

    • 4.5.1

      How to read program listings

    • 4.5.2

      The initialization section

    • 4.5.3

      Command line arguments

    • 4.5.4

      If statements

    • 4.5.5

      Parsing numbers

    • 4.5.6

      Exceptions

    • 4.5.7

      The control section

  • 4.6	Writing a Java class: the Gene class

    • 4.6.1

      The framework

    • 4.6.2

      Variables

    • 4.6.3

      Access control

    • 4.6.4

      The constructor

    • 4.6.5

      this

    • 4.6.6

      Getters and setters

    • 4.6.7

      Methods

    • 4.6.8

      toString

    • 4.6.9

      The simulation

  • 4.7	Building and running your program

  • 4.8

    Summary

  • 4.9	Projects and exercises

• 5	Regulatory Networks
  	Programs with several classes

  • 5.1	Gene transcription networks

    • 5.1.1

      Negative autoregulation

    • 5.1.2

      Feed forward loop

  • 5.2	Chapter preview

  • 5.3	Simulating a feed forward loop

    • 5.3.1

      Main program

    • 5.3.2

      The SimEvent class

    • 5.3.3

      The Promoter class

    • 5.3.4

      The Gene class

    • 5.3.5

      Exercises

  • 5.4	A flexible simulation program

    • 5.4.1

      ArrayList

    • 5.4.2

      Reading files

    • 5.4.3

      Exercises

• 6	A neural simulation
  	Inheritance, or relations between classes

  • 6.1	Chapter Preview

    • 6.1.1

      Programming topics

    • 6.1.2

      Biology topics

  • 6.2	The Morris-Lecar neuron model

    • 6.2.1

      Ion conductance

    • 6.2.2

      Calcium conductance

    • 6.2.3

      The leakage current

    • 6.2.4

      Potassium conductance

    • 6.2.5

      Potential

    • 6.2.6

      Advanced note

  • 6.3	Running the simulation

  • 6.4	Using a hash table for the parameters

    • 6.4.1

      The HashMap class

    • 6.4.2

      Extending HashMap

  • 6.5	The simulation

    • 6.5.1

      Overview

    • 6.5.2

      The Conductance class

    • 6.5.3

      The LeakConductance class

    • 6.5.4

      The CalciumConductance class

    • 6.5.5

      The PotassiumConductance class

    • 6.5.6

      Interfaces

    • 6.5.7

      Terminology and summary

  • 6.6	Running the simulation

    • 6.6.1

      The rest of the code

    • 6.6.2

      Experimenting with the simulation

  • 6.7	Fine points of inheritance

    • 6.7.1

      Exceptions in overridden methods

    • 6.7.2

      The difference between overloading and overriding

    • 6.7.3

      What about fields?

  • 6.8	Releasing your software

    • 6.8.1

      Move your class

    • 6.8.2

      Add documentation with Javadoc

    • 6.8.3

      Packaging the release

  • 6.9

    Exercises

  • 6.10	Type parameters

    • 6.10.1

      Classes for the units

    • 6.10.2

      Bounded type parameters

    • 6.10.3

      Extensions of parameterized types

    • 6.10.4

      Wild cards

    • 6.10.5

      Limitations

• 7	Biological sequences
  	Biological software packages

  • 7.1	Chapter Preview

  • 7.2	Biological sequences

    • 7.2.1

      Raw sequence data

    • 7.2.2

      Gene transcription

  • 7.3	Sequence file formats

  • 7.4

    BioJava

    • 7.4.1

      Installing BioJava

  • 7.5	Sample programs

    • 7.5.1

      Global sequence alignment

    • 7.5.2

      Viewing protein structure

• 8	Using web services

  • 8.1	Chapter preview

  • 8.2	Biological data online

    • 8.2.1

      Viewing sequences in Ensembl

    • 8.2.2

      Viewing sequences from NCBI

  • 8.3	Programmatic access to sequences

    • 8.3.1

      Courtesy when using common resources

    • 8.3.2

      Using URL objects

    • 8.3.3

      Acquiring sequence data

  • 8.4	Accessing BioMart

    • 8.4.1

      The underlying HTTP

    • 8.4.2

      Searching Biomart manually

    • 8.4.3

      XML

    • 8.4.4

      Manipulating XML in Java

    • 8.4.5

      A program to find BioMart data

• 9	Probabilistic sequence algorithms
  	Random numbers, and lambda expressions

  • 9.1	Chapter preview

    • 9.1.1

      Programming topics

    • 9.1.2

      Bioinformatics topics

  • 9.2	The typing monkey

    • 9.2.1

      The main program

    • 9.2.2

      Random numbers

    • 9.2.3

      The Typer class

  • 9.3	Smarter monkeys

    • 9.3.1

      Trigram models

    • 9.3.2

      Program structure

    • 9.3.3

      Extending the random number generator

    • 9.3.4

      The unigram model

    • 9.3.5

      Object persistence

    • 9.3.6

      NGram models

  • 9.4	Training the models

    • 9.4.1

      Data sets

    • 9.4.2

      Creating the models

    • 9.4.3

      The complete cycle

  • 9.5	Lambda expressions

    • 9.5.1

      What are lambda expressions?

    • 9.5.2

      Functional interfaces

    • 9.5.3

      Functional programming

    • 9.5.4

      Types in lambda expressions

    • 9.5.5

      Local values in lambda expressions

  • 9.6	Bulk data operations

    • 9.6.1

      Outline of a bulk data operation

    • 9.6.2

      Streams

    • 9.6.3

      Intermediate operations

    • 9.6.4

      Terminal operations

    • 9.6.5

      The complete ngram trainer

  • 9.7	Identifying unknown data

    • 9.7.1

      Calculating the probability

    • 9.7.2

      Adding biological sequence data

• 10	Alignment algorithms
  	Practical programming

  • 10.1	Sequence alignments

  • 10.2	Big O notation for algorithmic complexity

    • 10.2.1

      Exercise

  • 10.3	Dynamic programming

    • 10.3.1

      Exercise

  • 10.4	An alignment program

    • 10.4.1

      Setting up the program structure

    • 10.4.2

      The DPMatrix1 class

    • 10.4.3

      The dynamic programming nodes

    • 10.4.4

      Running the program

  • 10.5	Optimizing memory and performance

    • 10.5.1

      Increase the heap size

    • 10.5.2

      Profile the application

    • 10.5.3

      Garbage collection

    • 10.5.4

      Improve the algorithm

  • 10.6	Assertions

    • 10.6.1

      Adding assertions to alignment

    • 10.6.2

      Using assertions

    • 10.6.3

      Proper and improper uses

  • 10.7	Unit testing

    • 10.7.1

      Test driven development

    • 10.7.2

      Setting up the framework

    • 10.7.3

      Testing alignment

• 11	Genetic drift
  	Graphical User Interfaces

  • 11.1	Chapter Preview

    • 11.1.1

      GUI toolkits

  • 11.2	The finished program

    • 11.2.1

      Setting up the structure

  • 11.3	Genetic drift

  • 11.4	Enumerations

    • 11.4.1

      Defining an enumeration

    • 11.4.2

      Using an enumeration

  • 11.5	The population model

    • 11.5.1

      Random breeding

    • 11.5.2

      Random survival

  • 11.6	Developing the interface

    • 11.6.1

      GUI tools

    • 11.6.2

      The initial JFrame

    • 11.6.3

      Adding the controls

    • 11.6.4

      Summary

  • 11.7	The JavaFX interface

    • 11.7.1

      Principal differences

    • 11.7.2

      Starting FX development

  • 11.8

    Exercises

• 12	Chemotaxis
  	Threading

  • 12.1	Chemotaxis

    • 12.1.1

      Running the simulation

    • 12.1.2

      How chemotaxis works

  • 12.2

    Threading

    • 12.2.1

      Disadvantages of threading

    • 12.2.2

      Advantages of threading

  • 12.3	Genetic algorithms

  • 12.4	A threaded simulation

    • 12.4.1

      Modeling one bacterium

    • 12.4.2

      A pond full of bacteria

    • 12.4.3

      The user interface

  • 12.5	Simulating chemotaxis

  • 12.6	Simulating survival

    • 12.6.1

      Stopping a thread

    • 12.6.2

      Does it work?

  • 12.7	Synchronizing access

    • 12.7.1

      Synchronized methods

    • 12.7.2

      Deadlock

    • 12.7.3

      Synchronizing on objects

  • 12.8	Letting chemotaxis evolve

    • 12.8.1

      The Genotype class

    • 12.8.2

      Additions to the Bacterium class

  • 12.9	Other concurrency tools

    • 12.9.1

      Memory consistency

    • 12.9.2

      Atomic operations

    • 12.9.3

      Synchronized collections

    • 12.9.4

      Semaphores

    • 12.9.5

      Work queues

    • 12.9.6

      Futures

    • 12.9.7

      Executors

    • 12.9.8

      Completable futures

• 13	Scientific images
  	Reflection

  • 13.1	Chapter preview

  • 13.2	Image processing

    • 13.2.1

      Image formats

  • 13.3

    ImageJ

    • 13.3.1

      Counting cells

  • 13.4	Writing a plugin

    • 13.4.1

      The ImageJ plugin framework

    • 13.4.2

      Adding the plugin code

  • 13.5	The jar explorer

    • 13.5.1

      The JarExplorer interface framework

    • 13.5.2

      Setting up the tree

    • 13.5.3

      Examining the classes

    • 13.5.4

      Invoking a method

  • 13.6	Projects and Exercises

• 14

  Projects

  • 14.1	RNA folding

  • 14.2	Phylogenetic trees

  • 14.3	Multiple alignment

  • 14.4	Access to NCBI data

• Appendix
  • Amino acids
  • Nucleic acid bases
  • Codons
• Image credits
• Bibliography
• Tools and services
• Index