Tag Archives: newcastle

Announcing a Bioinformatics Kblog writeathon

(Reposted from Knowledgeblog.org)

The Knowledgeblog team is holding a ‘writeathon’ to produce content for a tutorial-focused bioinformatics kblog.

The event will be taking place in Newcastle on the 21st June 2011.  We’re looking for volunteer contributors who would like to join us in Newcastle on the day, or would like to contribute tutorial material remotely to the project.

We will be sending invites shortly to a few invited contributors but are looking for a total of 15 to 20 participants in total.

Travel and accomodation costs (where appropriate) can be reimbursed.

If you would like to contribute tutorial material on microarray analysis, proteomics, next-generation sequencing, bioinformatics workflow development, bioinformatics database resources, network analysis or data integration and recieve a citable DOI for your work please get in touch with us at admin@knowledgeblog.org

For more information about Knowledgeblog please see http://knowledgeblog.org.  For examples of existing Knowledgeblogs please see http://ontogeneis.knowledgeblog.org and http://taverna.knowledgeblog.org.

CASE PhD studentship in Bioinformatics available at Newcastle

A repost from Fuzzier Logic:

Where? – Newcastle University – School of Computing Science

What? – Development of Novel Computational Approaches to Mine Integrated Datasets for Drug Repurposing Opportunities

The blurb

We invite applications for a CASE PhD studentship in Bioinformatics at Newcastle University in the North East of England. The project is a 3-year EPSRC PhD sponsored by GlaxoSmithKline (GSK) and involves the development of novel methods of finding new targets for existing drugs using data integration.

Ondex is a data integration computational platform for Systems Biology (SB). The student will research the optimization and application of Ondex integrated datasets to the identification of repurposing opportunities for existing compounds with a particular, but not exclusive, focus in the infectious diseases therapeutic area. The student will also use the dataset to explore the interplay between microbial targets and perturbations in the metabolic and community structure of the human gut microbiome.

An ideal student will have a background in computing science, good programming skills, preferably in Java and an interest in biology and bioinformatics. Applicants should also possess an upper second class undergraduate degree. Only students who meet the EPSRC home student requirements are eligible for full fees, other EU students are only eligible to support for the fees. Students from outside the EU are not eligible to apply – please see the EPSRC website for details.

The studentship will start in October 2011, jointly supervised by Prof. Anil Wipat and Dr. Simon Cockell at Newcastle University, and Dr. Philippe Sanseau at GSK. The student will spend at least three months at GSK in Stevenage as part of the project. Home students are eligible for payment of full fees and an enhanced stipend of approximately £18,000 tax free. To apply, please send an email to [anil dot wipat at ncl dot ac dot uk] with CV (including the contact details of least two referees) and a cover letter indicating your suitability for the position. Please include “Application CASE PhD” in the subject of the email. Applications will be dealt with as they arrive – there is no closing date.

R courses at Newcastle

This announcement courtesy of Colin Gillespie one of our  lecturers in Maths and Stats (blogging here and Newcastle profile here):

The School of Maths & Stats are going to run two R courses this year (Thursday 7th & Friday 8th April 2011).
  • Course 1: Introduction to R. This course assumes no prior knowledge of R, programming or statistics.
  • Course 2: Programming with R. This course is a follow-on from the first course.
The aim of these courses isn’t to teach statistics, rather to introduce fundamental concepts of programming with R.

Places are limited, and on a first come, first served basis.

If anyone is interested please look at http://www.ncl.ac.uk/math/rcourse/ where they will find specific dates, more detailed information and costs.

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