| Nota di contenuto |
Cover -- Acknowledgements -- Preface to the Second Edition -- Contents -- 1 Introduction -- 1.1 From data to knowledge: the aim of bioinformatics -- 1.2 Using this book -- 1.2.1 About the coverage of this book -- 1.2.2 Choice of tools -- 1.2.3 Choice of operating system -- 1.2.4 www.bixsolutions.net -- 1.3 Principal applications of bioinformatics -- 1.3.1 Sequence analysis -- 1.3.2 Transcriptomics -- 1.3.3 Proteomics -- 1.3.4 Metabolomics -- 1.3.5 Systems biology -- 1.3.6 Literature mining -- 1.3.7 Structural biology -- 1.4 Building bioinformatics solutions -- 1.5 Publicly available bioinformatics resources -- 1.5.1 Publicly available data -- 1.5.2 Publicly available analysis tools -- 1.5.3 Publicly available workflow solutions -- 1.6 Some computing practicalities -- 1.6.1 Hardware requirements -- 1.6.2 The command line -- 1.6.3 Case sensitivity -- 1.6.4 Security, firewalls, and administration rights -- References -- 2 Building biological databases with SQL -- 2.1 Common database types -- 2.1.1 Flat text files -- 2.1.2 XML -- 2.1.3 Relational databases -- 2.2 Relational database design-the 'natural' approach -- 2.2.1 Steps 1-3: gather, group, and name the data -- 2.2.2 Step 4: data types -- 2.2.3 Step 5: atomicity of data -- 2.2.4 Steps 6 and 7: indexing and linking tables -- 2.2.5 Departure from design -- 2.3 Installing and configuring a MySQL server -- 2.3.1 Download and installation -- 2.3.2 Creating a database and a user account -- 2.4 Alternatives to MySQL -- 2.4.1 PostgreSQL -- 2.4.2 Oracle -- 2.4.3 MariaDB -- 2.4.4 Microsoft Access -- 2.4.5 Big Data and NoSQL databases -- 2.5 Database access using SQL -- 2.5.1 Compatibility between RDBMSs -- 2.5.2 Error messages -- 2.5.3 Creating a database -- 2.5.4 Creating tables and enforcing referential integrity -- 2.5.5 Populating the database -- 2.5.6 Removing data and tables from the database.
2.5.7 Creating and using source files -- 2.5.8 Querying the database -- 2.5.9 Transaction handling -- 2.5.10 Copying, moving, and backing up a database -- 2.6 MySQL Workbench: an alternative to the command line -- 2.7 Summary -- References -- 3 Beginning programming in Perl -- 3.1 Downloading and installing Perl -- 3.1.1 Older versions of Perl on Mac OS -- 3.1.2 Older versions of Perl on Linux -- 3.1.3 Installing Perl on Windows -- 3.1.4 Compilers and other developer tools -- 3.1.5 Before getting started -- 3.2 Basic Perl syntax and logic -- 3.2.1 Scalar variables -- 3.2.2 Arrays -- 3.2.3 Hashes -- 3.2.4 Control structures and logic operators -- 3.2.5 Writing interactive programs-I/O basics -- 3.2.6 Some good coding practice -- 3.2.7 Summary -- 3.3 References -- 3.3.1 Multidimensional arrays -- 3.3.2 Multidimensional hashes -- 3.3.3 Viewing data structures with Data::Dumper -- 3.4 Subroutines and modules -- 3.4.1 Making a Perl module -- 3.5 Regular expressions -- 3.5.1 Defining regular expressions -- 3.5.2 More advanced regular expressions -- 3.5.3 Regular expressions in practice -- 3.6 File handling and directory operations -- 3.6.1 Reading text files -- 3.6.2 Writing text files -- 3.6.3 Directory operations -- 3.7 Error handling -- 3.8 Retrieving files from the Internet -- 3.8.1 Utilizing NCBI's eUtilities -- 3.9 Accessing relational databases using Perl DBI -- 3.9.1 Installing DBD::MySQL -- 3.9.2 Connecting to a database -- 3.9.3 Querying the database -- 3.9.4 Populating the database -- 3.9.5 Database transactions and error handling -- 3.10 Harnessing existing tools -- 3.10.1 CPAN -- 3.10.2 BioPerl -- 3.10.3 System commands -- 3.11 Object-oriented programming -- 3.11.1 Object-oriented programming in Perl using Moose -- 3.12 Summary -- References -- 4 Analysis and visualisation of data using R -- 4.1 Introduction to R.
4.1.1 Downloading and installing R -- 4.1.2 Basic R concepts and syntax -- 4.1.3 Vectors and data frames -- 4.1.4 The nature of experimental data -- 4.1.5 R modes, objects, lists, classes, and methods -- 4.1.6 Importing data into R -- 4.1.7 Data visualization in R -- 4.1.8 Writing programs in R -- 4.1.9 Some essential R functions -- 4.1.10 The RStudio integrated development environment -- 4.2 Multivariate data analysis -- 4.2.1 Exploratory data analysis -- 4.2.2 Scatter plots -- 4.2.3 Principal components analysis -- 4.2.4 Hierarchical cluster analysis -- 4.2.5 Pattern recognition -- 4.3 R packages -- 4.3.1 Installing and using Bioconductor packages -- 4.3.2 The RMySQL package for database connectivity -- 4.3.3 Packages for multivariate classification -- 4.3.4 Writing your own R packages -- 4.4 Integrating Perl and R -- 4.5 Alternatives to R -- 4.5.1 S+ -- 4.5.2 Matlab -- 4.5.3 Octave -- 4.6 Summary -- References -- 5 Developing web resources -- 5.1 Web servers -- 5.2 Introduction to HTML -- 5.2.1 Creating and editing HTML documents -- 5.2.2 The structure of a web page -- 5.2.3 HTML tags and general formatting -- 5.2.4 An example web page -- 5.2.5 Web standards and browser compatibility -- 5.3 Programming for the web using Perl -- 5.3.1 Mojolicious::Lite -- 5.3.2 Debugging Mojolicious applications -- 5.3.3 Routes -- 5.3.4 Interfacing with databases within a web application -- 5.3.5 Getting user input via forms -- 5.3.6 Deploying a Mojolicious application -- 5.3.7 Going further with Mojolicious -- 5.4 Advanced web techniques and languages -- 5.4.1 Cascading stylesheets -- 5.4.2 JavaScript, JavaScript libraries, and Ajax -- 5.5 Data Visualization on the web -- 5.5.1 Using R graphics in Perl -- 5.5.2 Plotting graphs with Chart::Clicker -- 5.5.3 Plotting graphs with SVG::TT::Graph -- 5.5.4 Primitive graphics with Perl.
5.5.5 Drawing graphs and graphics using JavaScript -- 5.6 Summary -- References -- 6 Software engineering for bioinformatics -- 6.1 Unit testing -- 6.1.1 Unit testing in practice -- 6.2 Version control -- 6.2.1 The basics of version control -- 6.2.2 Centralized versus distributed version control -- 6.2.3 Git -- 6.2.4 Alternatives to Git -- 6.2.5 Hosting and sharing your code on the Internet -- 6.2.6 Running your own code repository -- 6.3 Creating useful documentation -- 6.3.1 Documenting command-line applications -- 6.3.2 Documenting Perl code -- 6.4 User-centred software design -- 6.5 Alternatives to Perl -- 6.5.1 Python -- 6.5.2 Ruby -- 6.5.3 Java -- 6.5.4 Using Galaxy -- 6.6 Summary -- References -- Appendix A: Using command-line interfaces -- A.1 Getting to the operating system command line -- A.2 General command-line concepts -- A.3 Command-line tips -- Appendix B: Getting started with Apache HTTP Server -- B.1 Installing Apache -- B.2 Apache fundamentals -- Appendix C: Setting up a Linux virtual machine in Windows -- C.1 Installing VirtualBox and configuring a virtual machine -- C.2 Using the VM -- C.3 Other uses of virtual machines -- Index.
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Building bioinformatics solutions [[electronic resource] /] / Conrad Bessant, Ian Shadforth, Darren Oakley
