The elevator pitch goes something like this:

“The project extends existing blogging tools for use as a lightweight, semantically linked publication environment. This enables researchers to create a hub in the linked-data environment, that we call knowledge or k-blogs. K-blogs are convenient and straight-forward for authors to use, integrating into researchers existing work practices and tools. The provide readers with distributed feedback and commenting mechanisms. We will support three communities (microarray, public health and workflow), providing immediate benefit, in addition to the long term benefit of the platform as a whole. Additionally, this will enable a user-centric development approach, while showcasing the platform as the basis for next generation research publishing.”

If this sounds like the kind of thing you’re interested in, Phil has made the full grant application that we submitted available online, on knowledgeblog.org. We would of course be interested in any comments or feedback. The proposal includes some technical details of what we hope to achieve, but I think that Ontogenesis has already gone some way to proving the worth of the system. It’s going to be great to provide additional tooling to support the process, and cement some of the inherent social contract with a proper workflow for publishing and review.

The  project starts almost immediately, and knowledgeblog.org will be the place to stay tuned for updates.

Application forms etc. are here

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
.

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

GeneSpring GX 11 is the third iteration after Agilent bought up Silicon Genetics, then decided to throw the unwieldy, quirky, but very functional GeneSpring product in the trash and start again with something built on Strand Life Sciences AVADIS platform.  We’ve been through versions 9, 10 and now we’re on 11.  There’s been plenty of bugs on the way, the most serious (to me) being the one where GeneSpring 10 managed to miscall the quality flags on Illumina data in 50% of the cases.  Not good, but at least fixed.

Many people have been griping on mailing lists about functionality missing in the new GeneSpring that existed in the old version.  I always think it’s a matter of familiarity with the software really.  I hadn’t really come across anything I couldn’t do in GeneSpring 11 that I could do in GeneSpring 7.  That was until yesterday.

I sat down with a customer yesterday to look at some microbial Nimblegen data.  GeneSpring doesn’t really deal with Nimblegen data very well, you are left with the choice of not analysing it in GeneSpring, or accepting there’s going to be a bit of fudging and some extra annotation steps in order to make the data useable as a ‘Custom technology’.  The customer, quite reasonably, asked if we could get the biological genome information (effectively gene annotations that are independent of the chip technology you’re using) loaded into GeneSpring.  And thus started a morning of fun and games.

GeneSpring 11 has a very handy import feature for biological genomes under Annotations>Create Biological Genome.  That is providing you want to choose one of their predefined organisms to download the information from NCBI.  There is *NO* route in the software to add another organism to this list, or do anything than use one of their check box limited organisms.  This is not a bug apparently, because in a separate part of the software (dealing with Pathways for an organism) you can pull this information directly from NCBI using the Taxon ID of the organism you’re interested in.  So why can’t you use it to download a biological genome?  Who knows…

One of the things I really liked about the old GeneSpring was the fact that it came with a manual a foot thick.   It told you how to do every single operation in the UI, it didn’t tell you anything about the order in which to apply them, but you could generally rely on it for an answer.  There was no such answer to this issue in the GeneSpring manual..

It transpires that if you really want to do this, the following, slightly insane process needs to take place:

1) Take this snippet of XMLishness:

<hexff version="1.0">
<object type="cube.plugin" version="1.0" handle="0">
 <key>type</key>
 <string>plugin.product.TaxID</string>
 <key>id</key>
 <string>TaxID</string>
 <key>data</key>
 <!-- taxID.xml for various organisms {{{ -->
 <dict>
 <key>Homo sapiens</key><string>9606</string>
 <key>Mus musculus</key><string>10090</string>
 <key>Rattus norvegicus</key><string>10116</string>
 <key>Anopheles gambiae</key><string>7165</string>
 <key>Arabidopsis thaliana</key><string>3702</string>
 <key>Bacillus subtilis</key><string>1423</string>
 <key>Bos taurus</key><string>9913</string>
 <key>Caenorhabditis elegans</key><string>6239</string>
 <key>Canis lupus familiaris</key><string>9615</string>
 <key>Citrus sinensis</key><string>2711</string>
 <key>Danio rerio</key><string>7955</string>
 <key>Drosophila melanogaster</key><string>7227</string>
 <key>Equus caballus</key><string>9796</string>
 <key>Escherichia coli</key><string>562</string>
 <key>Felis catus</key><string>9685</string>
 <key>Gallus gallus</key><string>9031</string>
 <key>Glycine max</key><string>3847</string>
 <key>Gossypium hirsutum</key><string>3635</string>
 <key>Hordeum vulgare</key><string>4513</string>
 <key>Macaca mulatta</key><string>9544</string>
 <key>Magnaporthe grisea</key><string>148305</string>
 <key>Medicago sativa</key><string>3879</string>
 <key>Medicago truncatula</key><string>3880</string>
 <key>Nicotiana tabacum</key><string>4097</string>
 <key>Oryctolagus cuniculus</key><string>9986</string>
 <key>Oryza sativa</key><string>4530</string>
 <key>Ovis aries</key><string>9940</string>
 <key>Pan troglodytes</key><string>9598</string>
 <key>Plasmodium falciparum</key><string>5833</string>
 <key>Pongo abelii</key><string>9601</string>
 <key>Poplar mosaic virus</key><string>12166</string>
 <key>Populus sp.</key><string>3697</string>
 <key>Pseudomonas aeruginosa</key><string>287</string>
 <key>Saccharomyces cerevisiae</key><string>4932</string>
 <key>Saccharum officinarum</key><string>4547</string>
 <key>Salmo salar</key><string>8030</string>
 <key>Schizosaccharomyces pombe</key><string>4896</string>
 <key>Staphylococcus aureus</key><string>1280</string>
 <key>Sus scrofa</key><string>9823</string>
 <key>Takifugu rubripes</key><string>31033</string>
 <key>Lycopersicon esculentum</key><string>4081</string>
 <key>Triticum aestivum</key><string>4565</string>
 <key>Vitis vinifera</key><string>29760</string>
 <key>Xenopus laevis</key><string>8355</string>
 <key>Xenopus tropicalis</key><string>8364</string>
 <key>Zea mays </key><string>4577</string>

 </dict>
 <!-- }}} -->
</object>
</hexff>

2) Add an entry

<key>Your organism name</key><string>NCBI Taxon ID</string>

after the Zea mays line

3) In your GeneSpring directory under this tree:

GeneSpring  GX11\bin\packages\marray\project\2.1

Create a folder called ‘plugins’ and save the edited XML above as a file called TaxID.plg

4) Restart GeneSpring and proceed to update your newly added Biological genome, which now appears in the list!

Actually, I have to say, I’m not sure I ever want to see that in a manual of a piece of software as expensive as GeneSpring…  And besides this still doesn’t work for me as advertised because GeneSpring, whilst aware of what an HTTP proxy might conceivably be, has no concept of what an FTP proxy might be – which is problematic when you need to connect to ftp.ncbi.nlm.nih.gov.  Brilliant!

These are now on Flickr and I apologise for the lack of quality, shooting indoors at MIT with no flash and shaky hands – but I hope they convey some of the spirit of the 2 days we spent there.

http://www.flickr.com/photos/eridanus/sets/72157622760324890/

We won a Gold Award!

Enquiries about the position to:

Liz Worthy, Senior Staff Scientist at the HGMC (eworthey@mcw.edu)

DESCRIPTION:
A Postdoctoral position is now open within the Human and Molecular Genetics Center (HMGC) at the Medical College of Wisconsin (http://www.mcw.edu/HMGC.htm). HMGC scientists work at the interface of genomics, bioinformatics, and clinical research using genomic approaches to understand disease, and translating this information from the laboratory bench to patients in our affiliated hospitals. The centers close affiliation with clinicians and researchers at nationally and internationally acclaimed medical centers and universities provides our researchers with a unique opportunity to impact patient care. Diseases under study are varied and include: end stage renal disease, hypertension, insulindependent diabetes mellitus, acute liver failure, neurocognitive disabilities, cancer, cystic fibrosis, metabolic syndrome, hereditary cataracts, myocardial infarction and various cardiac malformations. A variety of core resources exist within the HMGC including: Bioinformatics, High-throughput sequencing, Genotyping, Microarray, Proteomics, Gene Therapy, and Transgenics. The HMGC consists of 28.

POSITION DESCRIPTION:

The postdoctoral fellow is expected to make a significant impact in existing genomic data analysis methodology at the HMGC. She/He will work as part of a team developing methods for analyzing data from next-generation sequencing, including integration with genome-wide association studies, gene expression data, biological networks, and pathway data. She/He will then apply these methods to the ongoing study of a variety of complex genetic disorders within the HMGC and will have the opportunity to participate in projects integrating genomic datasets with clinical data, and will be able to develop new research projects at the interface between genomics and medicine.

MINIMUM POSITION QUALIFICATIONS:

Appropriate education and/or experience may be substituted on equivalent basis

The ideal candidate will will be enthusiastic, highly motivated, able to work in a team environment, and have strong communication skills. Applicants should hold a Ph.D. in Bioinformatics, Genomics, Genetics, or a related field; a degree in Computer Science with strong biology background is also acceptable. The ideal applicant will have Linux operating system experience and proven skills in computer programming; experience in bioinformatics techniques such as sequence assembly and comparative genomics, as well as experience in navigating and mining genomic data repositories such as NCBI and Ensembl etc. is also desired. Experience in next generation sequencing data analysis or statistical analysis of high throughput genomics data is a plus.

ESSENTIAL DUTIES:

• Perform complex analysis of genomic datasets with minimal supervision.
• Assist in the development and/or refinement of data analysis and integration methodology and pipelines.
• Record results of research studies; compile and analyze data; and prepare charts and graphs for presentation.
• Analyze, interpret, and present the results of these analyses, including manuscript preparation and publication.
• Review literature for related research developments and techniques and compile findings.
• Perform related responsibilities as required.

One of the things I’ve always been vaguely jealous of is the amount of these kinds of events that seem to exist in the USA – there’s a meetup for everything whether you’re interested in tech, science, hacking, or publishing.  People get together, talks are given, people interact over food or a coffee (or a beer if you’re lucky).

I used to go to 2600 and alt.ph.uk meetings back in my impressionable younger days, so outside of scientific conferences this is the first opportunity I’ve taken to sit in a room with a bunch of like minded people outside of my day to day work  to chew the fat on tech for an awfully long time.  This months theme (for the meetings are most definitely monthly) was databases.  Now I can’t get terribly excited about databases per se – SQL is fugly, I prefer MySQL over PostgreSQL for ease of use rather than functionality and these days if I could do it in SQLite I probably would, but nevertheless there was a really nice series of three talks in this themed session.

Ross Cooney (SuperMondays organiser extraordinaire and @rosscooney on Twitter) gave a speedy history of the database world, and a quick reminder of the things I have already forgotten about databases after not doing a lot of db development recently (like what ACID stands for – no it’s not an HTML compliance test, or a drug (you crazy Berkeley hippies)) and introduced the other two speakers for the evening.

David Lavery followed next (@dlavery62) with a review of both SimpleDB from Amazon Web Services and Google BigTable two cloud offerings for the post-RDBMS database world.  I particularly enjoyed the SimpleDB part of the talk, anything delivered via a RESTful interface (don’t bother trying to convince me it’s not really RESTful, I could not care less) looks like a good thing to me after trying to deal with the SOAP webservices world last year.

The final talk was of a far more academic slant with David Livingstone of Northumbria University who presented RAQUEL which is an open source implementation of some of the ideas in The Third Manifesto, which appears at first glance to be an ‘RDBMS done right’ according to modern relational theory (and not affected by legacy cruft from current popular SQL implementations).  Part middleware, part programming language, part educational tool I would like to have heard a little more about the implementation here.  We were treated to a lot of syntactical details (which had me in mind of a cross of SQL, Perl and R and therefore maybe not something you would want to necessarily spend all day doing), but they’ve only just released this to the world and are looking for people to engage and interact with their foray into OSS development.  It certainly generated the most questions from the gathered geeks!

After these a roadmap for the future SuperMondays was presented.  Although this was my first SuperMonday event, it was in fact their 12th.  It may have started in a (very nice!) restaurant in Newcastle a year ago around a table, but there were maybe 80 people in the theatre tonight which suggests it is going from strength to strength.  Newly incorporated as a Community Interest Company (saving buckets of paperwork over being a charitable organisation) the future for SuperMondays looks very bright indeed.  Very much looking forward to the next one!

Yeah, there’s no oxymoron of a face to face geek event, but if you only saw the tagline in your RSS reader maybe you read a little further because of it ;)  I should also say cheers to the Newcastle ARCSOC students who I had a couple of drinks with afterwards too (depriving myself of further SuperMondays sandwiches in the process), it was nice to see you all again!

You can also find SuperMondays on Twitter (@supermondays) and on Facebook too!

The only thing about FriendFeed is that whilst it aggregates a lot of personalised content from my cohort of tech-savvy friends, it hasn’t quite turned into an RSS aggregator par excellence.  A vast swathe of my online time is still spent consuming RSS feeds in Google Reader.  So as an incentive to start blogging again (with a low barrier of entry ;)) I thought I would share a few of my favourite feeds that keep me coming back again and again, some of which hopefully are novel and useful.

I organise my reads by broad themes, and the first one in Google Reader happens to be ‘Arts’.  This covers, for me,  contemporary art to music (which I won’t *cough*Torrentech*cough* go into) to literature (and by literature I mean Sci-Fi ;)) and some stuff in between.

First up is the BALTIC forthcoming events feed.  The BALTIC is a fantastic contemporary art gallery on the banks of the Tyne, which splits Gateshead (my stomping grounds) from Newcastle (where I actually work).  Housed in an old flour mill on the Gateshead side, the BALTIC is one of my favourite places in the North East and every time I go I feel privileged to have such a great gallery so close to home.  The feed itself serves up good notice of forthcoming exhibitions, but for the real skinny on lectures, workshops etc. then the Facebook group or mailing list tends to have more details than just the exhibitions.  It would have been nice if they hadn’t switched their RSS feed URL with zero warning in August though.  A last post detailing the new  URL would have been a nice touch.  Or maybe a PURL for the feed perhaps?  It took me a little while to notice as new installations don’t come around that often!

Charlie’s Diary is the excellent blog of Charles Stross – one of my favourite British SciFi authors.  Aside from the fact that he writes great fiction, this is a man who writes his own blog engine, loves vi, predates Linux and once was gainfully employed crafting crufty Perl scripts to provide one of  the earliest online payment systems on the internet.  This man is not only an author, but a geeks geek, and politically astute enough to understand the ramifications of advancing technologies.  This blog is worth a read, regardless of whether you are a fan or not.

The final two links in this category deal with my current mild obsession which is digital photography.  Having recently splashed out on a very low end digital SLR (a Nikon D40 if you care) the chance to marry obscene technological geekery with something vaguely artistic has been a powerful draw for me.  It’s lead to a number of magazine and book purchases, but there’s nothing like the internet for free and useful information.

So the Digital Photography School feed is first up.  For me this is just the best site for a continual stream of information for my new hobby.  Split into 3 main sections the site slices and dices it’s articles into “Photography Tips and Tutorials”, “Cameras and Equipment” and “Post Production”, I really only look at the first of these.  I won’t be making any more equipment purchases other than a tripod, remote shutter release, neutral gradient density filter, polarising filter, telephoto and macro lenses (and the depressingly expensive  50mm AF-S f1.4G Nikkor that I crave) for a while.  OK so it’s basically so that I don’t add any more expensive items to my Amazon wish list, and the fact that I can pretty much work out how to use Lightroom by myself for now.  I am completely awash in a world of f-stops, ISOs, apertures and shutter speeds, and it’s this site that is helping me through it currently.

The second is a proper photography blog – the feed of the Newcastle Upon Tyne Daily Photo site.  This is a photoblog of local (well to me!) sights, with two main contributors.  Now when these girls say ‘Daily’ they mean ‘Daily’ I don’t think in the months that I’ve subscribed they have ever missed an opportunity to post a view of Newcastle and its surrounds.  Yes, there’s been an occasional repost, but not one that I’ve seen twice yet!  Everything is covered from the Quayside, the city centre, pubs, bridges, the lot.  Sometimes there’s views of the city and places that I’ve just not noticed, other times I’ve had to grab the camer and go out and grab similar shots.  The photos might not always have stunning composition, but it’s just nice to be reminded that Newcastle is a beautiful northern city, proud of it’s heritage and definitely my favourite city in England.  A few of my own photos taken over the last few months have ended up in this gallery on flickr but I need to take some more.  I’ve also got some photos of Gateshead here and the Great North Museum (Hancock edition) here.  Next time they invite reader submissions, I’m going to see if I can get one of my shots in…

So yes.. my ‘Arts’ section, not so large you see!  Wait until I get onto the feeds in the ‘Geek’ section eh?

84 DRIVE FAILURE BOX #1, BAY1
102 VOLUME #0 STATE INTERIM RECOVERY
102 VOLUME #1 STATE INTERIM RECOVERY
102 VOLUME #2 STATE INTERIM RECOVERY
102 VOLUME #3 STATE INTERIM RECOVERY
102 VOLUME #4 STATE INTERIM RECOVERY
102 VOLUME #5 STATE INTERIM RECOVERY
84 DRIVE FAILURE BOX #1, BAY2
84 DRIVE FAILURE BOX #1, BAY3
101 VOLUME #0 STATE FAILED
101 VOLUME #1 STATE FAILED
101 VOLUME #2 STATE FAILED
101 VOLUME #3 STATE FAILED
101 VOLUME #4 STATE FAILED
101 VOLUME #5 STATE FAILED
84 DRIVE FAILURE BOX #1, BAY4
84 DRIVE FAILURE BOX #1, BAY5
84 DRIVE FAILURE BOX #1, BAY6
84 DRIVE FAILURE BOX #1, BAY7
84 DRIVE FAILURE BOX #1, BAY8
84 DRIVE FAILURE BOX #1, BAY9
84 DRIVE FAILURE BOX #1, BAY10
84 DRIVE FAILURE BOX #1, BAY11
84 DRIVE FAILURE BOX #1, BAY12

Pretty ugly eh?  It’s the kind of error that brings me out in a cold sweat every time I get emails from our users.  Generally complaints that the databases are running slowly, or that files are disappearing from directories, that home directories are empty, reports that the filesystems have become read-only.

Of course when I go to look at the machine the display apparently tells me that an entire box of drives (we have 2 boxes with 12 drives in) has suddenly failed.  The RAID volumes can’t maintain such a loss of drives, hence we INTERIM RECOVERY followed by STATE FAILED as more drives drop out of the array.

The weird thing is of course is that there’s nothing wrong with the drives at all, they’re sat there blinking little green lights at me telling me they are just fine.

The unit is an HP StorageWorks Modular Smart Array 1000, and I have to doubt the Smart moniker in this case, as it is the single most unreliable piece of hardware we own, apart from perhaps the HP blades it is attached to.  Apple RAID units, Transtec RAID units, all the RAID5′d servers seem to pretty much be able to hold themselves together, but not this one.

Every time this happens we get an engineer called out, they plug a serial console into the unit, reset the error states on the drives and volumes, reboot the RAID and everything comes up smelling of roses.  However trying to get them to send an engineer out is an exercise in frustration.  It would of course be possible to affect this fix ourselves, given a laptop with a serial port, and one of HP’s magical and deeply proprietary 259992-001 console serial cables.  Do we have one with our kit?  No.  How much do they cost? About £120.  How much did we spend on the kit in the first place?  Well over £100,000.

I will never, ever buy or recommend the purchase of another bit of HP kit as long as I am in the position to do so.  Grr.