Tag Archives: work

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.

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.

Job opportunity at the NERC Environmental Bioinformatics Centre

An email from an old colleague has just dropped in the inbox.  There’s a position going at my old place of work, in fact it’s my old job!  3 previous occupants – all of whom are still sane!  Seriously it was a great position, with a great group with lots of exciting things to get involved in.

Application forms etc. are here

Bio-Linux Developer and Bioinformatician

The Centre for Ecology & Hydrology (CEH), part of the Natural Environment Research Council (NERC), is the UK’s Centre of Excellence for research in the terrestrial and freshwater environmental sciences. We have sites at Wallingford, Bangor, Edinburgh and Lancaster.

The NERC Environmental Bioinformatics Centre (NEBC) offers bioinformatics and data management collaboration opportunities and support services to environmental scientists generating and using molecular data types.  The bioinformatician will join the NEBC team, participating and furthering our bioinformatics collaborations, playing an active role in our helpdesk, and working in the development and delivery of Bio-Linux.

You will have strong informatics skills as well as an interest in biological research. In addition to strong system administration skills, you will be fluent in Perl or a related language, and preferably will be comfortable using at least one additional programming language. Your interest in Linux customisation will enable you to play a leading role in the technical development of Bio-Linux. You will ideally be familiar with cluster and cloud computing. As well as enjoying working collaboratively in a team environment you will have a proven record of effective communication, both written and oral, with strong time management and organisational skills.

The salary for this post is £26,180 progressing to £29,410 per annum.  In addition NERC offers a public sector pension scheme, 30 days’ annual leave and 10½ days’ public and privilege holiday per annum.  We offer a flexible and supportive working environment and will encourage your continuing professional development as part of our career support.

Questions about the role can be sent to the NEBC directly: admin@nebc.nerc.ac.uk. Please return your completed application along with your CV and an up-to-date publications list to the Recruitment Team, People & Skills Section, Centre for Ecology & Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB Email: cehpersonnel@ceh.ac.uk

PhD position available at Newcastle

Reposted from Philip Lord’s blog ‘An Exercise in Irrelevance

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

Blogroll addition

So I’ve added a new blog from Hugo Hiden to the blogroll links. Hugo is the technical director of the North Eastern Regional e-Science centre (http://www.neresc.ac.uk), which is based in Newcastle University. We interact quite a bit whether it’s due to the CARMEN project or our Campus Grid or because of the fact we’re both sort of (but not quite) in the Computer Science department, but spend lots of our time there.

Hugo is one of the people (and there are many) who don’t subscribe to the philosophy that Open Source is necessarily best. Filling the shoes of the previous technical director (Savas Parastatidis, now at Microsoft) maybe this is unsurprising, but I think the blog will be extremely interesting if you’re wondering how things might be done in a parallel universe outside your OSS microcosm :)

The original ‘heads up’ on this exciting development came of course from Frank who is always there at the bleeding edge of anything ending in 2.0.