The Blog Swan

So this evening I went to my first SuperMondays event.  What is SuperMondays you ask?  Well it’s a social networking event for geeks in the North East.

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!

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.

When I was a youngster, fascinated with the IBM PC clones that existed in the back pages of my Dad’s electronics catalogues and the amazing specs (and price tags!) they had whilst I toiled away with a Dragon 32 (and later an Atari ST), I used to sit around and lazily spec out machines that could not possibly have existed at the time.  Sci-Fi computers if you will.   Things with such outrageous memory and disk that I thought I would never see the day.

Now for a paltry £15k we have a Dell R905 in the rack, replacing our 32 CPU G5 Xserve cluster.  Screenshots below because they make me happy :)

The rest of the day is basically going to be Simon and I pimping this out with software so we can start doing work on it.  And we do have a fairly big backlog of memory intensive stuff we want to do!

Oh it’s taken a while, but the 24″ iMac arrived today.  Monitor left is attached to the old G5.  Monitor right is a secondary screen for the iMac.

I *still* have less monitors on my desk than the PhD students!!

So this year, after eschewing the notion of going to ISMB we had been looking for a good, UK based conference with enough of an informatics slant to keep us interested, but with a bit more ‘real science’ than the continual stream of talks on algorithmic refinement that ISMB has become.

BioSysBio had been recommended, and not least because we had a Newcastle student member on the organising committee.

BioSysBio is a relatively new conference run by the Institute of Engineering and Technology.  I admit I had been largely ignorant of the IET, probably because I’m not an engineer of any sort, and it’s a professional body for the engineering community.  BioSysBio, being a conference largely focused on systems and synthetic biology actually falls quite well under the engineering remit – not just for the engineering approaches that are applied to synthetic biology, but also because sometimes, just sometimes this kind of work needs giant, room-filling robots.

The meeting this year was held in Cambridge in the UK, one of our most venerable university towns, giving the event a feeling of academic history despite being about possibly the most cutting edge of biological sciences.  Over three days a group of probably 250 people gathered in the Music Department to discuss, listen, type, debate and network.  A word to other conference organisers, holding the conference in the Music Department is a great idea when you have a conference venue designed for performance – the acoustics were great for talks.  The lack of power supplies however belied the number of concert goers that normally need to plug in a laptop and work whilst they listen.  A reminder to us all that it’s all very well packing our power adaptors when we go to a conference, but a four-way block/gang plug would make you a popular person indeed in situations like this.

I don’t want to run over all of the sessions, you can find the programme for the three days here.  I do however just want to rave about how good a conference this is, and share a few highlights.

At the moment BioSysBio is a great size, and is run as a single track conference with unconference style breakouts given their own slot.  A two hour slot on the second afternoon was given over to a number of simultaneously run workshops (I plugged for the ONDEX tutorial, because I work with some people who are on the ONDEX project – but still had no idea how to use the software).

Interestingly there was a really good balance between the systems biology and the synthetic biology sides of the track.  I was more impressed by the lack of laptops being sported during the talks, it meant that actual, real biologists were present mixing it up with the informatics and mathematics geeks.  This also showed through in the poster sessions.  It’s a refreshing change for a bioinformatician to see the science that has resulted from informatics based approaches, rather than having the implementation of the approaches being the primary concern.

My talks highlights came from a number of people and areas.  I found Julian Huppert‘s talk on “Four-stranded DNA: How G-Quadruplexes control transcription and translation” fascinating.  Here was a whole area of transcriptional control I had never even come across, mediated by DNA structures I had never heard of.  That’s one of those nice eye-opening moments at a conference, when the complexity of the systems you study is just laid bare in front of you by something new and exciting.  On the second day we had a talk entitled “Effect of pauses on transcriptional noise” from Andre Riberio, following on from a previous talk on RNAP the previous day by Marko Djordjevic.  The idea of patterns in transcriptional noise, caused by kinetic and spatial restraints really caught my imagination.  I really enjoyed Catherine Lloyds talk on CellML – we’re interested in both SBML and CellML at Newcastle, and it’s always nice to see speakers from both projects on the same billing.  The panel discussion on security and synthetic biology (and touching on DIYbio as well) was extremely enlightening and not just because of the fantastic talk by Drew Endy who I had the pleasure of seeing speak twice at the meeting.  On the final day there was much to chose from from Christina Smolke talking about building circuits with bits of RNA to Piers Millet from the UN talking about why we should care about securing synthetic biology.

This brings me nicely onto online coverage of the conference.  If you want to read blog posts about any of the talks, there’s just one place to go and that is to Allyson Listers blog at lurena.vox.com.  Ally, who we shall now refer to as the ‘Robot Blogger’, managed to have coverage of each talk online within minutes of them finishing, whilst apparently being able to type up notes from the talk immediately following this.  When Allyson spoke about her work on SAINT, Simon Cockell of FuzzierLogic picked up the blogging slack.

The conference organisers were fully Web 2.0 enabled.  We had a pre-existing room on FriendFeed that got heavily trailed on the first day, as well as a small contingent of Twitter enabled users contributing comments and commentary during the talks.  These were all aggregated with the hashtag #biosybio.  I think everyone agreed that whilst this is never the best way to present information from a conference (doing this on Friendfeed with an agreement between participants in a threaded discussion probably the best) I know that those of us who were twittering away were at least being thanked for it from others who could not attend.  That certainly kept me interested in how my wifi connection was doing throughout the day.  We also had the strange effect of some of our colleagues and former colleagues attending “The Influence and Impact of Web 2.0 on e-Research Infrastructure, Applications and Users” at NESC who were all using the hashtag #research3 and we even had some microblogging cross talk going with delegates there.  That was a new one for me certainly.

Despite not everyone on my Twitter subscription lists being a scientist, let alone ones interested in synthetic or systems biology, and despite posting hundreds of very geeky tweets, not a single person unsubscribed from my posting frenzy.  Either no-one is paying attention or people were happy to filter the noise for a couple of days, which I thought was great.

To sum up, it’s a great conference.  It will be great to go to it again next year in Oxford too.  I can’t remember the last time I attended every conference talk, even the 8.30am ones.  I can’t remember the last time I went to a conference and wasn’t tempted to have a post lunch snooze in the lecture theatre afterwards.  I can’t remember coming away from a conference so fired up and so keen to get back to work and start thinking harder about this years iGEM competition.  Actually the last conference I felt anything like this much fervour and excitement about was the excellent (but never repeated) O’Reilly Bioinformatics Technology Conference in Tucson in 2002.

Next year, if you’re in the field, or even vaguely interested in the field, beat a path to this conference in Oxford.  Beg, borrow or steal the cash.   I will see you there.

Thanks Debian Stable.  Living up to your name.  My first machine to reach 1000 days of uptime. :)

I don’t think there’s much debate over this in our family.  I have inherited many useful traits from my mother that is for sure, but when it comes to geeking out, well those genes are all from my dad.

As if any evidence ever needed to be provided for this, here is a picture of his small, but immaculately clean and ordered electronics ‘den’.

I’d like to say I had his organisational and filing skills to boot, but I don’t.  Neither do I have his flair for electronics.  But I think we’re largely driven by the same desires to take things apart to see how they work, and then try and stick them back together again.  Although I tend not to care if they no longer work at this point, my dad is almost certainly not only going to have them working, but working better than before…

More equipment and general geekery can be found on Flickr

So we took delivery this morning of a shiny new HP 2710p (not for us, but for Matt). Matt couldn’t contain his excitement (or let us deliver it to him at lunch) so came up to the office.  At this point we plugged it in and turned it on.  Time on the clock was 11am.

Now, I don’t know if it was a problem with Vista, the tablet, or what.  HP’s ‘first boot’ setup makes Dell’s look streamlined.  The machine, after deciding which OS to install (64bit or 32bit), created a rescue partition, populated the rescue partition, asked us for some passwords, installed some software.  It rebooted maybe 7 times in all.

It finally booted into a workable Vista desktop at 1.15pm.   2 hours and 15 minutes for a new machine to boot into a useable configuration is apalling.  After 20 minutes we were already joking that we could have installed Ubuntu and configured it AND downloaded enough development tools to keep Matt happy in that time.  We had no idea that it would finally boot in front of us over 2 hours later during lunch.

I feel for any consumer that has to go through this process.  It’s not impressive.  By 3pm Matt was already prepping to wipe it in favour of an XP/Ubuntu dual boot.  Oh the complete install package?  Over 20GB disk was gone by the time it had finished.

It’s become quite trendy recently to talk about ‘cloud computing‘.  This is largely due to the fact that the Amazon EC2 system has been apparently well hyped recently, despite the fact other vendors (notably Sun and IBM) have been selling compute for years.  Whilst this excites the blogging masses quite a lot, I suspect cloud computing is still going to take a while to be useful to the bioinformatician who still values a tight link between his terabytes of data and the compute they’re meant to be crunched on.

Various European countries and the academic institutions that make them up already offer compute to scientists at the Grid level – everything from compute clusters for research groups, to the ‘campus grids’.  A step up from this are the NGI (National Grid Initiatives) of which the National Grid Service is the UK’s contribution.  It always surprises me when people get excited about paying for access to commercial services, when free services exist on the doorstep.   Complete with free training.

Now I see that the various European NGIs are looking at ways to support European wide research by coordinating and combining their efforts.  The European Grid Initiative Design Study is currently running and according to its project director looking to make the infrastructure ‘available seamlessly’.  I wonder how much of the ‘cloud computing’ ideal the EGI will take on board.  Anyone who has been on a training course to use these resources currently will know that ease of access probably hasn’t been the watchword in the past, but more of an effort to understand how the various parts of the middleware sit together in order that it can be used at all.

For some reason using the academic infrastructure in place for scientific computing makes more sense to me than going to a commercial concern.  The chances are the NGS et al. are going to be far  more familiar with the challenges of deploying scientific software in Grid environments than Amazon ever will.

I don’t often feel compelled to post links to columns, but even as (as described in the article) a casual coder at best, this is a really fascinating insight into the fall and fall of Windows as an attractive development platform.

From ars technica, a site I often forget exists, but perhaps should visit more often