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.â€
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! 
Following on from my last post for getting PostgreSQL up and running nicely on Mac OS X, my next task was getting it playing nicely with ruby on rails - I’m off on a rails course next week so I’m getting stuff ready.
It appears that there is currently two/three gem packages for using postgresql with ruby: postgres, ruby-pg, and pg - and from what I can make out, they’re all maintained by the same team now, (postgres was the original package, but it got abandoned - ruby-pg and pg are the replacements). As such, i’ll go with the newer ruby-pg gem…
sudo env ARCHFLAGS="-arch i386" gem install \
ruby-pg -- \
--with-pgsql-lib=/opt/local/lib/postgresql83 \
--with-pgsql-include=/opt/local/include/postgresql83
Then finally, when writing the database.yml entry for connecting to postgresql, we have to define our adapter as follows:
development:
adapter: postgresql
database: test_dev
encoding: unicode
host: localhost
user: XXXXX
password: XXXXX
timeout: 5000
This type of guide is all over the internet, but I’m too lazy to search for one every time I want to do this. So here’s a brief overview of how I got PostgreSQL set-up nicely on Mac OS 10.5…
Setting Up Our Environment
Using a text editor of your choice, add the following lines to the bottom of the /etc/profile file (you’ll need to be an administrator to do this):
# MacPorts
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
# PostgreSQL
export PATH=/opt/local/lib/postgresql83/bin:$PATH
Now before we move on, make sure that you have MacPorts installed.
Continue reading ‘Install PostgreSQL on Mac OS X Leopard’
Dropbox is a great service, I’m using it happily to keep my files in sync across multiple computers - I’m even using it to keep all of my passwords in sync, but I’ve thought of another great use… How about syncing my Things database between my macs (as this is my to-do list manager of choice)?
This is not fully tested yet, (just thought of it this morning) so i’ll update a bit later and report on as to wether things goes completely mental, but the way I’ve done this is as follows…
Make sure Things is completely shut down, then open up a terminal and type in the following commands:
cd ~/Library/Application\ Support/Cultured\ Code/
This moves us into the correct directory. First, to be on the safe side - we’ll take a backup of our files…
Now just move the Things directory into your dropbox and create a symbolic link in its place.
mv Things ~/Dropbox/
ln -s ~/Dropbox/Things Things
Fingers crossed this should have the desired results!
Update: It works!!! 
On the second computer all you need to do to get the ball rolling is to close down Things, open up a terminal and type the following commands:
cd ~/Library/Application\ Support/Cultured\ Code/
rm -rf Things
ln -s ~/Dropbox/Things Things
Note - my 2nd mac only had a fresh install of Things - no data. I installed it, opened it up (so the initial database was created), then did the above.
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