Here’s my take on the basics of it and why you would want this - there’s really LOTS more there!!!

The first thing Biocep is (that’s not really advertised much on the site) is that it offers a vastly improved interface to R that has the following tools:

• Built-in spreadsheet like functionallity
• Built-in code editor (jEdit)
• Plug-in architecture for creating custom interfaces to things (similar potential to Matlab’s GUIDE)

There are other R gui’s out there (i.e. Mac and Windows R spring to mind) - but they are not as slick as this.

The second thing biocep gives is that it allows you to run R instances on remote machines (i.e. up in the “cloud”, or on clusters or grid systems in your work place / institute), from your desktop and be able to work collaboratively with other people using fully shared sessions (i.e. both of you can play with shared data, talk and see all of the visuals the other person is seeing all in real-time - it’s really impressive to watch).

Seriously, if you work with R, check it out!

“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!

One of the tools that I currently need (for the thesis work) is R and the BioConductor libraries. So here’s a quick run down on getting them up and installed on Hardy…

First up, run these commands in a terminal:

sudo apt-get install build-essential g77 gfortran
sudo apt-get install refblas3 refblas3-dev zlib1g-dev
sudo apt-get install r-base

This will then install the R base packages and some of the BioConductor packages, along with the gcc and fortran compilers and some other libraries that will be required for the next step.

sudo -s
R

Now at the R prompt, type the following…

source("http://www.bioconductor.org/biocLite.R")
biocLite()

Now sit back for a few minutes while your system configures BioConductor for you.

I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…

Log into your system and open up a terminal, then follow these steps…

sudo gedit /etc/apt/sources.list

Add the following lines to the end of the file:

# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux

Save and close the file, now back at the terminal type the following:¹

sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden

Next step is to set-up your environment for Bio-Linux…

sudo gedit /etc/bash.bashrc

Add the following lines to the end of the file:

# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc

Save and close the file.

That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available)² so it might be worth checking the version numbers before installing things.