Category Archives: About me

Thoughts on a year in industry

A year ago I left the safe environs of academia and decided to move to industry.  I said farewell to my final salary pension, my Mac-centric mode of life, my newly-purchased house and the place that had been my home for the last 7 years to go return to Oxford and enter a world dictated by the cold logic of business.

Why did I move?

I think quite a few people were wondering this at the time.  Aside from the fact that 2011 had started as a most abysmal year (personal issues, not professional) there were a number of factors leading to my departure, but on the face of it the move may have seemed rash.  The Bioinformatics Support Unit at Newcastle University was running very well, publications were flowing, costs were being recovered to the satisfaction of the Faculty.  I had a great set of friends, colleagues and co-workers.

One of the things about bioinformatics support work is that it is, by it’s very nature, diverse.  This is great for not getting bored day to day, but not so great if you want to specialise in a field.  My work was split mostly between arrays and NGS (and mainly arrays) alongside the financial management of the Unit, student supervision (several PhD students and Masters students) and a dozen or so odd little projects that come your way in that kind of job.

My heart however has always been with genomics.  My favourite part of my PhD was always the sequencing.  In the hot-lab, up to my elbows in acrylamide and isotopes, all for the joy of pulling the autoradiograph film from the developer and spending the next couple of hours typing it into DNAStar before applying whatever gene/exon/splice-site prediction software I had committed to that day.  The future, to me, looks like it’s going to be heavily flavoured with NGS.

I had decided a long time ago never to enter industry, the by-product of a difficult year at Glaxo as a sandwich student.  I hated the feeling of being the smallest cog in a giant, impenetrable, deeply impersonal, multinational pharma.  From the people who I saw there, struggling with their own academia to industry transitions, to daily pickets from animal rights groups, to people who on handing in their notice, were marched from their offices to be dispatched from the premises without even a chance to pick up their personal belongings.  It didn’t seem like it was such a great place to be.

In late 2010 I started to get approaches from recruiters, all the positions were with NGS firms, or NGS related firms.  Some still around, some now counting down the days to their demise.  After a couple of months of weighing up whether I wanted to commit to the jump, the perfect job advert crossed my desk.  For the first time, I phoned a recruiter.  And that job was with OGT.

A year later, I thought it might be nice to summarise what I thought of the change.

What does the role entail?

No longer ‘bioinformatician at large’ I now have responsibility for developing  and returning the data to academic and commercial customers from our NGS analysis pipelines. We have built an extensive exome analysis pipeline which analyses not just exome samples, but also does comprehensive trio analysis and analyses cancer samples. A lot of data passes through this pipeline, and I couldn’t have done it without my fantastic sandwich student David Blaney, who I hope has had a much better year out  in industry than I did.  We’ve built an RNA-Seq pipeline too, shortly to be launched as a service.

I’m involved in a number of grant programmes internally, from solid tumour cancer diagnostics for stratified medicine, to pathogen screening and host/pathogen interactions – all from an NGS perspective.  We have a Genomics Biomarkers team as well, and they obviously have an increasing need for NGS approaches.

So what is the same?

Well I’m still doing bioinformatics. Arguably I’m doing more bioinformatics than in my previous role. I still get to interact with customers, although this took a while to be direct, rather than mediated via the sales team. I think you have to earn a certain amount of trust when entering a new role, but having done nothing but talk to customers for 7 years, I didn’t initially appreciate that there might be good procedural reasons for having an intermediate layer of communications with customers.

This is still one of the most satisfying parts of the role, delivering results and analyses back to researchers or commercial customers is great. Especially when you’re getting great feedback back about the quality of the data, and the findings from it.  Even better when they come up at a conference, shake your hand and tell you about the papers that have been submitted.

This is one thing about doing a lot of exome sequencing work for rare diseases – you get a lot of diagnostic power, and consequently a lot of hits. My name still goes on papers, we have just had a paper accepted that comes out in the AJHG in August and favourable noises from a pre-submission enquiry with a very high-impact journal for another.  Both exhibiting (we believe) absolutely novel classes of discovery from exome data.

What is different?

I talk to people from a much wider background at work. No longer talking to just biologists and computer scientists and fellow bioinformaticians, I now get to talk to enthusiastic people in the sales and marketing departments. I’m now much more intimately connected to the lab again, thanks to the both the R&D and services work.

It helps that OGT has a touch over 60 employees, it’s small enough to feel genially personable. I actually get to talk to the VP’s and CEO. Reguarly.

I get to travel more. This was something of a self-imposed rule at Newcastle – when you’re managing your own finances, trips to conferences don’t do much for the balance sheet. They simply don’t generate any revenue. Now the reasons have a much more financial focus, if I go away, I go away with one of the sales team. We do roadshows, conferences. I am now one of those people who stands on the company booth and talks to you, rather than the person who goes to a conference to listen to talks. However you are there to generate leads, not listen to talks. The cost of going must be balanced against the gains from the leads.

This is another aspect that has been very different. I have had an increasing interest in the business side of the life sciences for some time, but lacking any practical experience. This is now changing, I now understand how a business operates, what the margins need to be on a sale, the balance between selling products and selling services.

Because of the size of OGT I get exposure to this, I doubt it would happen in a larger company. I get involved in product development, I help to write product profiles, I’ve developed, and continue to develop, marketing materials for the website. These are all new skills for me, and I love to learn.

Another thing I’ve noticed is the makeup of the company is very different to academia. I work in a phenomenally talented group of computational biologists, who are skilled in software design, software development and all facets of bioinformatics analysis.  But not everyone has a PhD. Not everyone has a biology background.  And these are things I took for granted  in academia. If anything I have become more and more convinced that a PhD is of little consequence, especially for people who, like me, have switched discipline after getting it.  My colleagues are people who have worked in the more quantitative fields of accounting or investment banking, but retooled for bioinformatics, and have done so with aplomb.

Social networking changes

I think most people who interact with me online will have noticed that I don’t blog, tweet or participate in BioStar as much anymore.  I spend a lot of time on SeqAnswers, and my RSS reader is now top heavy with NGS related blogs, but participation is down.

There  are just commercial pressures which mean I can’t always blog about what I’m doing, and believe me there are some things at work I do under CDA/NDA that I would really love to talk about, but it’s not that I can’t blog about it, I can’t even talk to you about it over a pint of beer.  This is something I have had to accept about the commercial environment.  The IT policy at work is incredibly strict, to maintain the ISO information security standards that we have.  I’ve learned to adapt to this, and the Windows-centric environment.

The biggest issue though? Inability to get to papers.  Oh how I took for granted the access to papers I had at Newcastle.  I just want to say a big thank you to everyone who has sent me a paper on request in the last year, you have been invaluable to me, and it is deeply appreciated.

Was it worth it?

Absolutely.  Life at OGT is hectic, pressured but deeply rewarding.  I have the focus that I wanted, but with the diversity of a new set of challenges.  I think I’ve been very lucky to settle into a company that is the perfect size and makeup to transition gently from academia into the commercial world.  It might not be for everyone, but I will say I wish I had done it sooner.  I harboured doubts about industry, but they were predicated on my experiences with a giant company.  Sitting now in a position that is in a long-established  SME that is on a sound financial footing (as opposed to giant multinational, or precarious start-up), I wonder what I was concerned about.

23andMe kit ordered

So today I took a look at my savings account for ‘frivolous’ things, wondered what I could do with the money and split it between a couple of nights in a hotel in Manchester for a gig next week, and a 23andMe kit. This is something I’ve been wanting to do for a long time, previously thwarted by a lack of cash.

Watching Genomes Unzipped unfold and seeing a number of my Twitter/FriendFeed/BioStar chums get their spit analysed has been interesting, but since my day to day job now involves hunting down variations in clinical samples from exome sequencing projects, the subject of what might be lurking in my own genome has started to exhibit a morbid fascination.

I will say straight up, that if I had the money and there was an established DTC exome offering, I’d just get my exome sequenced and analyse it myself. However there is admittedly a little professional interest in how 23andMe present the data, as well as finding out more about what might be in store for me as I approach (if I have not already entered ;)) middle age.

I haven’t decided what I might do with the data (in terms of public release) when I receive it, I’m going to have a bit of a think and a read before the saliva kit arrives. Interestingly I’m feeling quite apprehensive about the results even at this stage, we will see how that develops too.

Knowledgeblogging

This week we had some welcome news (by we I mean Simon Cockell, Phil Lord and others). A proposal we had submitted to JISC has been funded. This is the first research funding I have received after significant input in the bid process, as opposed to being included as a co-I for specific bioinformatics expertise. As such it’s a bit of a departure for me, but something I’m very much looking forward to spending time on over the next year.

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.

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

7 things

Well thanks to Knirirr for perpetrating the blog equivalent of a chain letter on me by requesting that I not only reveal 7 interesting and random facts about myself, but then exhort 7 other people to do the same thing.  Interesting information is largely subjective, so if you don’t find the following 7 points of interest, I’m sorry, but not entirely surprised.

1) My favourite place in the world is Miyajima Island, which has such an uninspiring Wikipedia entry that I won’t even link to it.

It’s no secret that I love Japan and have been lucky enough to visit twice, and this is my favourite place in my favourite foreign country.  Miyajima is home to beautiful shrines – both Shinto and Buddhist, the most impressive torii, free roaming deer, lushly forested peaks, monkeys – and I want to go back there.  Right now.  It’s pointless trying to talk about the place without gushing, just go and have a look at some pictures and marvel.

2) I could turn vegetarian tomorrow with no regrets.

I don’t eat much meat these days, the by-product of my girlfriend being of the ‘don’t eat meat’ persuasion.  When you live with a vegetarian, you don’t get much leeway in what gets cooked for dinner.  Consequently my cookery skills with meat are lapsing, but my repertoire of vegetarian dishes grows ever larger.  Those who know me well know that I indulge in meat when I eat out with great relish, but after 18 months of living together, if I had to turn vegetarian tomorrow I could do it.  Liking tofu and the existence of Quorn products, does make this more tolerable I admit.  Mycoprotein FTW.

3) If I hadn’t been a biologist I would have been an archaeologist.

Ideally I would have been an astrophysicist, but my maths would never have been good enough for that I fear.  Now I cohabit with an archaeologist and can live the dream vicariously!

4) I don’t worry about the threat of terrorism.

For someone who grew up convinced the world was going to end in an apocalyptic blast of ‘mutually assured’ atomic destruction, worrying about a handful of nutters with amateur skills they’ve gleaned from the Anarchist Cookbook doesn’t seem like a productive use of my fear glands.  And no amount of governmental fear-mongering is going to change that.

5) I’m one half of an NT/AS relationship.

I’m the NT part.  This means I’m a neurotypical person, but my girlfriend has Asperger’s Syndrome (AS).  I think this is a relatively rare situation as male Aspies outnumber female ones by 10:1.   It annoys me intensely when I hear people say how they ‘wish they had Asperger’s’ because they think it would confer some ubergeekesque affinity with maths or technology.     Asperger’s is a fascinating part of the autistic spectrum from a scientific point of view, but I wouldn’t wish it upon anyone.  I blog about this pseudonymously elsewhere.

6) My proudest scientific and career moment was having my PhD work (and very first paper) published in Nature.

Just don’t ever ask me about the way the author list is ordered.   It’s a shame that it was the result of the worst four years of my professional life (even though my first post-doc was nothing to shout about either).  I still love developmental biology, and think it’s still the most fascinating and beautiful field in the biological sciences.  I’m happy to be a bioinformatician now – the lab bench probably wasn’t for me and I’m glad it only took 6 years to realise that.

7) My current off-beat side interest is in DIYbio.

The idea of part-time geneticists and amateur molecular biologists working in their homes in the same way that amateur astronomers, or coders or electronics engineers is genuinely exciting to me.  In the last couple of weeks DIYbio has had press all over the place from AP and New Scientist.  If you’ve ever had the hankering to build your own electrophoresis apparatus at home, then this is the community to join.   The mailing list is also loaded with iGEM participants, which is always interesting.

OK so I suggest that the following 7 people might like to offer me insights into their life!  Simon at Fuzzier Logic, Ally at The Mind Wobbles, Frank at peanutbutter, Phil at An Exercise In Irrelevance, Nic at Dropbars, Jen at Genes and Aging and  Simon at Stumbling Towards Something.  The last two are merely a hint to the authors to start blogging again.  That’s about all the people I personally know blogging, although I was tempted to fill this with friendfeed contacts instead :)

2009 – a real year of celebration in science

I doubt there’s a biologist alive that hasn’t realised that 2009 marks a significant bicentennial – the birth of Charles Darwin, a man whose legacy is one of the most profound of any scientist who has ever lived.   Conveniently it is also the 150th anniversary of the book that is he is most famous for, “On the Origin of Species”.

A good hub for information on the celebrations would be the Natural History Museum’s Darwin200 site.

I was glad leafing through Chris Miller’s blog today to find out that I’m not the only scientist who has actually never read this book.   I actually downloaded the text from Project Gutenberg some years ago and stuck it on my iPod (in the days before I carried a smartphone) with the intention of reading it.   It was too long for the iPod reader, so I never got around to it.

In the absence of any formalised New Years Resolutions I promise to go out and find a nice hardbound copy to grace my bookshelf.  And read it too.

However, it’s not the only scientific anniversary being celebrated.  For those people who are more interested in staring at the sky than staring at living organisms 2009 is also the International Year of Astronomy.

Again, there’s a fantastic dropping off point from the IAU and UNESCO at astronomy2009.  But why is this being celebrated?  In this case it is the 400th anniversary of the first use of an astronomical telescope by Galileo Galilei, whose legacy is at least as awe inspiring as that of Darwin’s.

With an amateur telescope setup with a CCD camera/webcam capable of producing pictures rivalling that of a 200″ telescope in the 1950’s I always feel it’s a shame that more people don’t stare in awe at the sky.  I particularly liked this story on the Physics World site, about how a group of people are going to build a replica of Gallileo’s telescope and image through it, to show what the man himself might have been capable of resolving.

I find it interesting that these are both thinkers who proposed theories that were against the prevailing religious orthodoxy, and in Darwin’s case some even now failing  to be accepted by some people of a more closed minded religious persuasion.   Maybe all Darwin needs is another 250 years?

Whilst I’m making ad hoc resolutions – I will also use this year to  interact more with my local astronomical society, a group of people who I am in frequent email contact with, but have yet to pitch up to the society meetings to join.

I’m proud to be a scientist, and I’m proud of the wonderful achievements science has made, so it will be nice to use these two excellent celebrations to push my own knowledge forward a little more.  And not just focused around the computerised science I spend my time on.

So what does happen when you talk to a spam bot?

I get occasionally harassed on Yahoo! IM by spam bots.  Normally I don’t bother with them, if I wanted to be more restrictive in my privacy settings I know I could be.  I just close the window and get on with my day.   Today I thought I would have a little chat with one.  I didn’t know they actually spoke back!  They normally just pop up with some gibberish and a URL.  This one took a while to get to the point:

irwin: ncgod   U around
Dan: no
irwin: Hey Dan
Dan: lol
irwin: it’s me Emily¨µëÔè
Dan: i dont know an emily
irwin: I know u probably dont remember me LoL, its been awhile
Dan: no, my memory is just fine
irwin: hey i am finally free this week , we should get together
Dan: i dont think so, i dont know you
irwin: my boyfriend is gone & I’m looking to have some fun  ¶¦ æ•http://www.%61d%75%6c%74%68%6fo%6b-%75p%73.ne%74
Dan: well i’m not
irwin: Lets get crazy ¼Ï¤øðhttp://www.h%6f%6f%6b%2d%75%70s-r%2d%75s.c%6f%6d u up for it?
Dan: no
irwin: To remove your ID visit Ú¢ãÕÎhttp://affiliatediamond.net/unsubscribe.asp

Wistfully I imagine there is an Eliza style backend to that, but I doubt it :)

Diet update

As my little diet badge has dropped off the front page I thought I’d reinstate it.  Current progress is that I’m 12 stone or just under depending on when I weigh in (woo!) and no longer ‘overweight’ using my BMI as a guide.  About 12 pounds to go I think until I come off the diet :) Steady loss of 1lb/week at the moment which is a daily deficit of 500 cals (3500cals/lb fat!).

<img style="border: 0px;" src="http://www.fourmilab.ch/cgi-bin/HackDietBadge?t=1&b=53616J7465645W5W6Q69QQW086169592W396Q63274WFKKK724KK0F942F36FW9J689Q836F420JF4Q93JJF1G2501G3F9K9W17GW842Q63J68392K90W8JK2J7W40362WW6Q78K"

The ‘interview suit test’

Well I’ve been meaning to do this for a while.  It has been particularly noticable the last few times I have tried my (only) suit on that it just doesn’t fit.  I haven’t been able to do up the top button of the shirt, I haven’t been able to fasten the clips on the waistband of the trousers and the belt looks ridiculously short when on.

This suit was bought specifically for my Newcastle interview which must have taken place in December 2004.

This morning I have tried it on again – and magically – it fits.  The trouser waist is still a touch tight – but fits, my shirt can be buttoned fully without choking me, and when it’s all on it looks like it actually is my size.  The belt is 2 clear notches tighter!  Currently I’m hovering around 12.5 stone – which means I was probably 12 stone when I came to Newcastle – as the suit was a gorgeous, comfortable fit when I bought it.  Clearly the lack of walking to and from work, and a lack of clubbing and badminton has been the cause of my weight gain over the last 3 years – as to be honest I’m probably leading a much healthier food and drink life than I was in Oxford.

Anyway, a happy diet milestone for me – one that I was aiming for.  Hopefully the next time I try it on I will be out shopping for a tighter belt :)

Diet

I haven’t been talking here much about my diet as to be honest I find it intensely interesting and would write about nothing else, but I appreciate that other people don’t feel the way. Last week I got half way to my weight loss for my New Years resolution – 22 lbs or 10 kilos depending on your metric/imperial preference.

My Hackers Diet badge is for the last fortnight and will remain updated with my progress I believe!