Tag Archives: bioinformatics

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.

Bioinformatician post at NEBC, CEH Wallingford

This came through on a mailing list from the group I used to work for whilst I was at CEH in Oxford, and I thought it might be of interest:

 

We are recruiting for a new bioinformatician to join the NEBC group at
CEH Wallingford (nebc.nerc.ac.uk).  This is an open-ended position
available immediately.  We think this role might be ideally suited to an
ambitious new postdoc with experience of biological data analysis (esp.
high-throughput sequencing, metagenomics) and programming knowledge in
Linux.  If you know of anyone who fits this description please pass this
mail on to them.  The deadline for applications is 3rd April.

The successful candidate will primarily be working on data analysis,
development of new tools and scripts, and developing documentation and
training resources as part of our NBAF-W remit
(nbaf.nerc.ac.uk/nbaf-wallingford).  There will also be the opportunity
in time to branch out and become involved in the range of group
activities including involvement in megasequencing projects
(www.microb3.eugenomicobservatories.org), data standards (gensc.org,
mibbi.orgenvironmentontology.org) data sharing (biosharing.org,
isa-tools.org), cloud computing platforms (cloudbiolinux.org) and more.

Full information on the role, requirements, how to apply, and links to
further information are all on the CEH website:

http://www.ceh.ac.uk/personnel/Bioinformatician-vacancy.html

Please feel free to contact us directly with any queries related to the
role (admin@nebc.nerc.ac.uk).  Queries regarding the application process
should be directed to SSC.

Bioinformatician post at NERC Environmental Bioinformatics Centre (NEBC)

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.

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.

CASE PhD studentship in Bioinformatics available at Newcastle

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.

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

CENTRE FOR ECOLOGY & HYDROLOGY
Based at WALLINGFORD
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
.

Bioinformatics position at Human and Molecular Genetics Center (HMGC) Medical College of Wisconsin

Posting this for an old colleague of mine from my PhD days.  I can’t believe I have colleagues that date back to 1995…

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.

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The IET BioSysBio Conference 2009

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.

On procrastination

So  I was on IRC today talking to a guy from the Creative Commons group – always kind of interesting and we shared some common neuroinformatics ground by way of CARMEN (me) and the Neurocommons project (him).

I declared happily after our exchange that this meant that IRC was in fact still useful as a work tool (you will find me on #bioinformatics on freenode.net) and not just a means of diversionary procrastination, at which point one of the other channel regulars posted this informative URL from Psychology Today:

http://psychologytoday.com/rss/pto-20030823-000001.html

The fact that I subsequently needed to blog about this really doesn’t count as procrastination.  Does it?