“Modern bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. Building Bioinformatics Solutions provides a comprehensive introduction to this methodology, explaining how to acquire and use the most popular development tools, how to apply them to build processing pipelines, and how to make the results available through visualisations and web-based services for deployment either locally or via the Internet. The main development tools covered in this book are the MySQL database management system, the Perl programming language, and the R language for statistical computing. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. This advanced textbook is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.”

The book that I am a co-author on, Building Bioinformatics Solutions is shortly going to be available on Amazon (UK) and Amazon (US) as well as other countries.

If you’re looking for an introduction to some of the tools used in the field of Bioinformatics (programming, databases, data analysis) or even just looking for a general introduction to Perl programming, MySQL or R why not check it out.

Still here and after more?!?! Why not head on over to bixsolutions.net - the companion site for the book, and take a peek at what’s on offer.

Now get off my lawn!

If you want a somewhat pretty picture of your DBIC schema (with relationships drawn, of course), install GraphViz, SQL::Translator, and DBICx::Deploy from the CPAN, and then run:

$ dbicdeploy -Ilib MyApp::Schema ~/graphs GraphViz

~/graphs will then contain a .sql file that is actually a png of your schema. Rename it and see your schema in your favorite png viewing application.

via

About once a year I need to migrate a medium-sized web application using MySQL to Oracle.

Usually it’s to prepare a successful intranet application for a move to a formally supported production environment - and in Silicon Valley, that usually means Oracle.

I was apologizing to Monty at OSCON this year about my latest migration project away from MySQL.

His surprising response was, “It’s not a bad thing. I don’t mind hearing about conversions because successful migrations demonstrate that people don’t have to worry about database lock-in.”

Here’s some notes on doing migrations.

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First we need to create a sequence for the ID’s:

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CREATE SEQUENCE "S_COMMENT_ID"
START WITH 1
INCREMENT BY 1
CACHE 10;

Then we create the table and the required trigger:

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CREATE TABLE "COMMENT" (
  "COMMENT_ID" NUMBER(10,0) NOT NULL, 
  "COMMENT_BODY" VARCHAR2(1000), 
  "USER" VARCHAR2(100), 
  "CREATED_DATE" DATE, 
  CONSTRAINT "PK_COMMENT" PRIMARY KEY ("COMMENT_ID")
);
 
CREATE OR REPLACE TRIGGER "TR_COMMENT_ID" 
BEFORE INSERT 
ON COMMENT 
REFERENCING NEW AS NEW OLD AS OLD 
FOR EACH ROW 
BEGIN 
  IF(:new.comment_id IS NULL) then 
  SELECT S_COMMENT_ID.NEXTVAL 
  INTO :new.COMMENT_ID 
  FROM dual; 
  end IF; 
END;
/
ALTER TRIGGER "TR_COMMENT_ID" ENABLE;

And there you go - an auto-incrementing primary key… Damn that’s a lot more code to write than a simple ‘auto-increment’.

Edit: An alternative when using SQL Developer is to create your table, select it, then go to the ‘Triggers’ tab. In there you will find a useful ‘Actions…’ button where you can create a new trigger linking your tables primary key to a sequence.