If, like me, you didn’t make it to ASHG this year (although the company was there launching our NGS services!) you may be interested to know that there are a number of panel discussion up on Vimeo. No embedding allowed so you will have to click the tasteful ASHG logo to get to them!
I couldn’t help but notice in my GenomeWeb email deluge this morning that a position has opened up at the Bioinformatics Support Unit in Newcastle. I didn’t really make an announcement in my blog, but this is partly because I no longer work there! I now work for Oxford Gene Technology which I may find some time to write about soon.
Simon Cockell (blog, twitter), who worked with me throughout my time at Newcastle was appointed manager of the BSU when I left, and consequently his post is now available.
The BSU engages in a lot of diverse bioinformatics work and it’s an ideal post for someone who values supporting researchers in their quest to leverage high throughput techniques for biological studies. Job posting is below.
Newcastle University
Newcastle upon Tyne
£27,428 – £35,788
The Bioinformatics Support Unit is a successful cross-Faculty service providing high quality scientific support for a range of bioinformatics projects.
You will have experience of a range of Bioinformatics techniques, to work in the Unit on the development and delivery of scientific projects and liaison with relevant academics.
You should have at least a first degree in a relevant science related subject and preferably a PhD. You will have previous experience in bioinformatics support and an understanding of UK research funding procedures.
For an informal discussion on this opportunity, please contact either Dr Simon Cockell (Senior Experimental Scientific Officer), 0191 222 7253, simon.cockell@ncl.ac.uk or Professor Neil Wipat (academic lead), 0191 222 8213, anil.wipat@ncl.ac.uk
Via the Software Carpentry blog I see Newcastle University is hosting a ‘Programming for Scientists’ on Monday the 20th June, under the banner topic of ‘Effective use of programming in scientific research’.
From the blurb:
“Programming is becoming an increasingly important part of scientific research, yet many scientists are self-taught programmers with little formal training. This means that we are often unfamiliar with simple tools that can make programming and dealing with data faster, more reliable and more reproducible. This event is a day-long workshop to develop awareness of the skills and tools that help make computing more efficient and provide results that are less prone to error. If you’ve ever thought “Surely there must be a better way to do this”, then this is the event for you!”
Hopefully there will be a good take-up for this, it’s something we would quite like to have offered ourselves at some point at the BSU. Having taught biologists to program some time ago I know that it is possible to enthuse and encourage non-coders to start grappling with research problems relatively quickly and is the kind of professional development I think most research scientists should consider at some point.
Anyone interested in a bioinformatics post in the Oxford area?
A job has come up in my old group at the Centre for Ecology and Hydrology. Details linked here.
Looks ideal for a person with an interest in NGS and metagenomics though, working with both the NERC Environmental Bioinformatics Centre (NEBC) and the NERC Biomolecular Analysis Facility (NBAF).
Questions regarding the role may be addressed to Dawn Field and Tim Booth via the group address: admin@nebc.nerc.ac.uk. Closing date for applications is June 3rd.
(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.
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.
For the first time in many years I find myself the owner and maintainer of a set of Mailman mailing lists on behalf of Knowledge Blog this time. Mailman is a great piece of free software, but even the packaged install under Ubuntu (10.04.1 LTS in this case) is not without a couple of gotchas. In particular this installation was not archiving any of the email to our public mailing list (not so great for transparency!).
Despite seemingly have the correct setup on the list, on going to the archives page users were greeted with the uninformative, and definitely incorrect error:
“No messages have been posted to this list yet, so the archives are currently empty.”
My inbox has evidence to the contrary. A look at /var/lib/mailman/logs/error
shows this:
Nov 29 13:30:00 2010 (2426) Archive file access failure:
/var/lib/mailman/archives/private/knowledgeblog-discuss.mbox/knowledgeblog-discuss.mbox [Errno 13] Permission denied: '/var/lib/mailman/archives/private/knowledgeblog-discuss.mbox/knowledgeblog-discuss.mbox'
Nov 29 13:30:00 2010 (2426) Uncaught runner exception: [Errno 13] Permission denied: '/var/lib/mailman/archives/private/knowledgeblog-discuss.mbox/knowledgeblog-discuss.mbox'
Indeed the “private” directory in this case was owned by user ‘root’. By default on Ubuntu mailman runs as user ‘list’, so a quick:
sudo chown -R list /var/lib/mailman/archives/private/
worked a treat. In order to then generate the archive with the missed messages, all you need is a quick:
sudo /var/lib/mailman/bin/unshunt
One of the groups I support at work is rather wedded to FileMaker Server Advanced for hosting their databases. I understand this, they use the databases to hold strain information for their yeast experiments, ordering information for the lab and some image data. No-one needs to learn SQL to use it, and FileMaker Server Advanced allows them to serve their databases up across the campus to both FileMaker itself and also expose them on the web.
However, if you’ve ever had the misfortune of attempting to install FileMaker Server Advance you will realise that it needs a lot of encouragement to actually *work*. This particular reinstall was caused by the timely death of an ageing G5 Xserve.
First of all, a couple of hints that I’ve not seen anywhere else on the FileMaker forums to address common installation problems. For the record I installed it on a desktop machine running OS X 10.6.4
The problem I’ve hit time and time again with FileMaker Server Advanced is getting the IWP (Instant Web Publishing) working. When Filemaker installs, it required you to be running Apache, and have a certain set of firewall ports open. However it will invariably fail to correctly test the Apache installation and accept it. Whilst it gives you the option to come back later and do it, this will also never work. If you poke around online there are many many solutions offered up to this problem, mainly to do with the httpd.conf file. However the problem is a lot more straightforward, and must affect pretty much every single person who attempts to install this.
When FileMaker Server Advanced installs it creates a new system user called fmserver. This is the identity under which all the database services run. When it comes to setting up IWP, the ‘test’ it performs on the Apache installation is to attempt to install a couple of files to /Library/WebServer/Documents (this was exposed by perusing the Apache logs). This will never work as the fmserver user does not have sufficient privileges to write *anything* to this directory as it is drwxrwxr-x and owned by root, with group admin.
The solution then is simple and obvious, you need to add the fmserver user to the admin group. I haven’t seen this solution anywhere else online and hope that somebody might find it useful. After this procedure I uninstalled and re-installed FileMaker Server Advanced, and everything works as advertised now. The short incantation is (as an admin user):
$ dscl localhostcd /Local/Default/Groupsappend admin GroupMembership fmserverexit