Scientific web programming Part 6

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Scientific web programmingPart 6

• Putting it all together

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MySQL and PHP

• Whats the use of database?
• If you cant offer customized views?
• If you cant search it?
• If you cant modify it?
• Luckily theres PHP
• Use forms to get users preferences
• Process forms to build custom SQL queries

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Where we left off
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Getting the user involved
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This is getting complicated
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When things go wrong

• What is your SQL statement is wrong?
• Solution Mysql_error() and mysql_errno()

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SQL error handing
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Beyond querying

• SQL DML SQL Data Manipulation Language
• Querying
• SELECT fields FROM table WHERE field
  value ORDER BY field
• Editing
• UPDATE table SET field value WHERE field
  value
• Deleting
• DELETE FROM table WHERE field value
• Inserting
• INSERT INTO table (field) VALUES (value)

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Beyond data manipulation

• SQL DDL Data Definition Language
• Create databases, tables
• Alter databases, tables, columns
• Manipulate indices
• Work with stored procedures

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Questions before we continue?
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Furthermore

• Some pointers for further developing your PHP
  skills
• PEAR standard library
• Object oriented programming
• Processing RSS feeds
• JPGraph charting
• Native code

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PEAR

• PHP Extension Application Repository
• Other people have written libraries, too
• You can download them and use them
• http//pear.php.net/
• Dont go re-inventing the wheel

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PEAR packages
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Object oriented programming

• Advanced encapsulation
• Useful for longer-term, large-scale projects
• Not useful for proof-of-concept apps
• Initially takes longer
• The bigger and longer the project, the larger the
  pay-off
• Every class you write gets better
• Need a strategy for refactoring

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OOP in NetBeans
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RSS

• RSS RDF Site Summary
• RDF Resource Description Framework
• Computer-people like TLAs
• TLA Three-Letter Abbreviation
• Use fopen() to read from any URL
• Parse XML content from RSS feeds
• Add instant newsfeeds to your site

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PubMed

• Based on LastRSS
• RSS black box library for PHP
• http//lastrss.webdot.cz/
• Add literature feeds to your site
• http//lab.bcb.iastate.edu/sandbox/jlv/PubMedRSS/P
  ubMedRSS.php?qArabidopsis
• Written by John Van Hemert (jlv_at_iastate.edu)

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Other applications
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GraphViz

• Graph creating library - http//www.aditus.nu/jpgr
  aph/

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GraphViz in practice
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I still want more!

• You got it ?
• Command-line utilities
• E.g. GraphViz
• Connectivity to .NET
• http//us2.php.net/manual/en/book.dotnet.php
• Connectivity to Java
• http//us2.php.net/manual/en/book.java.php
• PHP extension development

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Using GraphViz
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Where to from here?

• Exercises on covered material
• BCBLab involvement
• Learn applied bioinformatics skills
• Small projects
• Databases, PHP, GUI design
• Also Perl, Fortran, VBA
• Microarrays, protein folding, ecology
• Mentoring by graduate students

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Questions

• http//lab.bcb.iastate.edu/training/webdev/nmsu