Monthly Archives: May 2010

Job opportunity at the NERC Environmental Bioinformatics Centre

An email from an old colleague has just dropped in the inbox.  There’s a position going at my old place of work, in fact it’s my old job!  3 previous occupants – all of whom are still sane!  Seriously it was a great position, with a great group with lots of exciting things to get involved in.

Application forms etc. are here

Bio-Linux Developer and Bioinformatician

The Centre for Ecology & Hydrology (CEH), part of the Natural Environment Research Council (NERC), is the UK’s Centre of Excellence for research in the terrestrial and freshwater environmental sciences. We have sites at Wallingford, Bangor, Edinburgh and Lancaster.

The NERC Environmental Bioinformatics Centre (NEBC) offers bioinformatics and data management collaboration opportunities and support services to environmental scientists generating and using molecular data types.  The bioinformatician will join the NEBC team, participating and furthering our bioinformatics collaborations, playing an active role in our helpdesk, and working in the development and delivery of Bio-Linux.

You will have strong informatics skills as well as an interest in biological research. In addition to strong system administration skills, you will be fluent in Perl or a related language, and preferably will be comfortable using at least one additional programming language. Your interest in Linux customisation will enable you to play a leading role in the technical development of Bio-Linux. You will ideally be familiar with cluster and cloud computing. As well as enjoying working collaboratively in a team environment you will have a proven record of effective communication, both written and oral, with strong time management and organisational skills.

The salary for this post is £26,180 progressing to £29,410 per annum.  In addition NERC offers a public sector pension scheme, 30 days’ annual leave and 10½ days’ public and privilege holiday per annum.  We offer a flexible and supportive working environment and will encourage your continuing professional development as part of our career support.

Questions about the role can be sent to the NEBC directly: Please return your completed application along with your CV and an up-to-date publications list to the Recruitment Team, People & Skills Section, Centre for Ecology & Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB Email:

PhD position available at Newcastle

Reposted from Philip Lord’s blog ‘An Exercise in Irrelevance

PhD Studentship, 2010

EPSRC PhD Studentship Building a logical model of biology: the Ontology of Mitochondria

For this project, you will use cutting edge technology designed for the Semantic Web, and apply it to the new field of systems biology. Specifically, you will develop an OWL ontology, a formal, logically specified model, to describe the mitochondria, a subsystem of the cell. You will use this to integrate large amounts of real-world data, to search for inconsistencies and produce a predictions about the underlying biology. From a computing perspective, this will result in insights both about the technology, and its scalablity; from a systems biology perspective, you gain understanding of the value of models which are wider than traditional mathematical models; from a biomedical perspective, you may gain insight in the functioning and behaviour of a medically important system of the cell.

This is a challenging multi-disciplinary project; applicants are not expected to understand all its aspects at the outset; as a result, it is of interest to those from either a computing science, computational biology or bioinformatics background. Any experience of ontologies, modelling or mitochondrial biology will be an advantage, but is not required. A willingness to learn is critical; students will spend significant time in both a computing science and biology environment, and will become familiar with both.

You should have either a First or 2.1 in Computing Science, a Biological Science or Mathematics, and a distinction level Masters degree in a related subject. Equivalent experience will also be considered.

Depending on how you meet the EPSRC’s eligibility criteria, you may be entitled to a full or a partial award. A full award covers tuition fees at the UK/EU rate and an annual stipend of £13,290 (2009/10). A partial award covers fees at the UK/EU rate only.

For further details, please contact Phillip Lord

On the joys of a local

It’s been a while since I had a pub that I would consider to be a local, even in Oxford I existed as a vagrant between a number of venues that I liked, dependent on budget, day of week and proximity to home.

Gateshead, or at least the part I live in, is full of pubs.  None of them I wish to frequent.  It’s not a matter of being a snob, I would happily drink in any of them providing they served anything other than lager and John Smith’s.  I have drunk in a number of my geographical locals, mainly the ones with pool tables, but spent more time in the local snooker club than anywhere else.

It’s a bit more conducive to go drinking in Newcastle where it’s not hard to find a pub with real ales to drink.  The normal Friday night haunt for many years has been Bodega, a beautiful pub that always has a decent selection of well kept beers.  It’s part of the Sir John Fitzgerald’s chain, which has a number of venues across the North East, and hasn’t neglected the fact that it’s customers might like something other than a fizzy lager once in a while.

Recently however we have switched our allegiances to another SJF pub, the fantastic Bacchus – more centrally located than Bodega, but with a wider selection of beers.  They also do a semi-regular event where they invite a brewery to come along on a Sunday to showcase a range of real ales from their catalogue with a matching course of food.  These have grown from 4 courses with 4 pints to a more sedate 8 courses and 8 half pints run over about 4 or 5 hours on a Sunday afternoon.  They have also picked up the CAMRA ‘Tyneside Pub of the Year’ award two years running.  Attending these events and spending an increasing amount of time in the pub means we’ve become quite well acquainted with the pub manager Andy.

The last two of these events at Bacchus have been from the amazing ‘one-man and his wife’ Yorkshire Dales Brewery and last weekend there was an event from the Highland Brewing Company.  We had tickets for this, and admittedly they are not cheap and of a very limited number, but we were unable to attend.  It was the Newcastle Beer and Cider Festival recently and we had studiously avoided the Highland brewery beers on the grounds we knew we were going to be trying them the following weekend.  How wrong we were.

On Tuesday I had an email from Andy saying they had missed us at the event, and whilst they could not offer us a refund, offered us a free lunch at the pub.   Consequently yesterday we spent the afternoon at the pub with a free Sunday roast, dessert, and a completely free run of the bar.  I don’t think we abused their hospitality too much, but I wonder how many other establishments would have made this kind of offer?  Fortunately there was still a selection of Highland beers on, and we still got to pick up our complimentary half pint porter glass (and bottle of delicious 9% porter).  Happy customers indeed.

It might not be the most local of locals for me, but if you’re in Newcastle sometime, Bacchus comes very highly recommended.  Great beer selection (and yes they cater for you lager lovers too), good whisky selection, good food, great staff and a policy of looking after their customers.

You can find Bacchus here