the life and times of a code monkey
Here’s the slides of another presentation I gave at work just before the Christmas break - this time on some of the development tools and resources that i’m using in my work: git and github.
The general gist is a basic introduction to both git and github, for developers who are already using version control (i.e. cvs or svn) but have yet to try distributed version control tools such as git.
I’ve always fancied trying my hand at a bit of home brewing but never actually found the guts to get myself a kit. Well, this time I finally went through with it and I’m now the proud owner of a starter home brewing kit!
I got the kit from the folks at The Happy Brewer in Bedford, it was very reasonably priced, and they were very friendly and happy to explain what was needed to be done to a complete novice. If you live near the Bedford area and fancy having a go yourself I’d happily recommend them.
That there is potentially 40 pints of Woodfordes Wherry, a very tasty beer sold at the local near the Sanger Institute - fingers crossed I’ll do a good job of it. This is the first fermentation step, in about 4-6 days I can move it into the barrel, then it’s a 3-4 week wait for the finished product. Will update with news on whether I killed myself (and anyone else brave enough to try it) soon! 
Last week I enjoyed some time up in Edinburgh for the International Workshop on Portals for Life Sciences (IWPLS ‘09), hosted at the e-Science Institute. It was a good workshop - there were good presentations, lively debates, and good social planning for the evenings!
I have to admit that quite a lot of the content of the workshop was completely irrelevant to me and went straight over my head at times, but I did enjoy it, and it’s good to hear what other people are doing.
I was there for two reasons, first was an interest in the content of the workshop, and second was that I was one of the people presenting a lightning talk! The content of my talk was pretty different to most of the other presentations - they were mostly about grid computing and development of portal interfaces for said grids - whereas mine was about the architecture I developed for the new Sanger Mouse Resources Portal.
It seemed to go down pretty well, it got a couple of laughs, no one fell asleep and quite a few asked questions at the end, so I was quite happy at that. Here’s the slides from the talk, just in case anyone would like to take a look. Copies of all the presentations from the workshop can be found here.
I went to an event called Cloudcamb last night (I love working in Cambridge) organised by Matt (ta very muchly), the evening was very good and informative, but the one thing that really stood out for me was a very interesting presentation on the Biocep project that anyone who uses R (or would like to use R) should be interested in.
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:
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!
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)
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! 
Okay, really bad pun…
Just come across this website Open Source Food. It’s yet another social networking site, but the difference with this one is that it is centered around one of my favorite things - Food!
Should be well worth a look for a few interesting recipes.
Amazing Recipes. Delicious Food. Beautiful Photography. Created and rated by you and fellow food-lovers from all over the world. Open Source Food is your gastronomic hub where every visit will bring inspiration and a rumbling belly…
These are a great idea for a quick and easy dessert when there’s nothing else to hand (they saved me last night)! Cheers to Celia for the recipe.
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