Was I really involved in writing something that sounds this classy?!?!
“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! 
Ack is a grep alternative, written in pure Perl, using Perl’s regular expressions to do your searches (just one of the long list of reasons to use this over grep). I think i’ll be using this then…
ack is a tool like grep, aimed at programmers with large trees of heterogeneous source code. ack is written purely in Perl, and takes advantage of the power of Perl’s regular expressions.
via
TableKit is a great javascript library for making your HTML tables fully editable. However, one problem is that you can’t add or delete rows from the tables…
I came up with a solution to this not so long ago, but it still had a problem - TableKit caches the tables on loading, so after we update the table body (adding or deleting a row) the sorting and editing of the table is completely screwed! 
However, with a little more work, and some help from one of the guys in the office - we’ve finally got this cracked!
Continue reading ‘Adding/Deleting Rows in TableKit Tables Revisited’
What a great idea - will give this a bash next week…
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
Oracle is a great RDBMS, but the fact that searches against the database are case-sensitive can be a pain in the butt. Here’s how you can make searches case-insensitive…
Continue reading ‘Remove Case-Sensitivity in Oracle’
This post has now been updated. Please head over to the new post for something better…
Following on from my previous post on how to integrate the excellent TableKit into your Catalyst webapp (to make your data tables dynamically editable), here’s how i’ve gone about adding ajax inserts and deletes so that you can add and remove data rows in your tables.1
Continue reading ‘Adding/Deleting Rows in TableKit Tables’
Found this small selection of tips that can come in use whilst working with Catalyst…
read more
Catalyst is an MVC web-development framework for Perl, very similar in concepts, ideas (and even some of the implementation) to Ruby on Rails. I’m using Catalyst a lot in my job now, and one of the first challenges that i’ve had to go through is making dynamically editable tables for some of the views we are using (in other words, Ajax driven edit-in-place tables).
Following a short Google, there seemed to be only two ready-made options I could see: one, using the Catalyst controller module Catalyst::Controller::ROSE::EIP; or two, by integrating and using the stand-alone javascript package TableKit.
Continue reading ‘Making Editable Tables With Catalyst and TableKit’