Opiniomics

bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Category: opinion (page 1 of 9)

With great power comes great responsibility

Recently I published a blog post about a fairly simple test to find out whether you have “short” protein predictions in your bacterial genomes, and predicted that some of these short peptides may be the result of unresolved errors in long-read, single molecule assemblies.

Perhaps not surprisingly, there was a reaction from the PacBio community over this, and here is my response.

Before I begin, I just want to say that, whilst most people see me as some kind of Nanopore fan-boy, the reality is I am a fan of cool technology and that includes PacBio.  The hard facts are that I have spent around £200k on PacBio sequencing over the last 18 months, and about £20k on nanopore in the same time period.  I also encouraged our core to buy a PacBio Sequel.  So I am not anti-Pacbio.  I am, however, anti-bullshit 😉

In addition, my blog post wasn’t about problems with technology per se, it was about problems with people.  If you don’t know errors are there, you might not correct them, and if you believe company hype (for example that PacBio data is Q50 after polishing) you might believe your assembly is perfect.

It isn’t.  They never are.

Let’s dive into some data.  The three PacBio genomes I chose in the last blog post are:

AP018165	Mycobacterium stephanolepidis 
CP025317	Escherichia albertii 
ERS530415	Yersinia enterocolitica

if you search GenBank genomes for these, there is only one Mycobacterium stephanolepidis genome, but there are 39 Escherichia albertii genomes and there are 176 Yersinia enterocolitica.  Many of these will be sequenced on different technologies, which allows us to do a comparison within a species.

Escherichia albertii 

I downloaded the 39 genomes from GenBank, and ran the process I described last week.  For the complete genomes, this is what the data look like, ordered from lowest number of short peptides, to greatest:

Accession Technology Contigs # proteins # short
GCA_001549955.1 Sanger+454 1 4299 19
GCA_002285455.1 Sanger+454 1 4157 19
GCA_002285475.1 Sanger+454 1 4295 28
GCA_002741375.1 PacBio 1 (plus 6 plasmids) 5126 79
GCA_002895205.1 Illumina+454+Ion 1 4423 83
GCA_000512125.1 PacBio 1 4482 106
GCA_002872455.1 PacBio 1 (plus 3 plasmids) 4984 124

Sure is unlucky that PacBio assemblies are at the bottom of the table isn’t it?  Of course, Sanger is the gold standard, and many will be asking what the Illumina assemblies look like.

Let’s look at the next ten genomes, which are not complete, but are the least fragmented:

Accession Technology Contigs # proteins # short
GCA_002109845.1 454 25 4758 93
GCA_001514945.1 Illumina 43 4237 82
GCA_002563295.1 Ion 44 4531 143
GCA_001514965.1 Illumina 50 4390 86
GCA_001515045.1 Illumina 53 4480 110
GCA_001515005.1 Illumina 59 4963 117
GCA_001514645.1 Illumina 63 4470 84
GCA_001514685.1 Illumina 70 4209 68
GCA_001514925.1 Illumina 73 4464 84
GCA_001514905.1 Illumina 78 4622 113

What I think is worth pointing out here is that the PacBio genomes in the first table, which are complete, have about the same number of short proteins as the Illumina and 454 assemblies in the second table, which are fragmented.  We would usually expect fragmented assemblies to have more short proteins because the contig ends would interupt ORFs.   Indeed, compared to Sanger complete assemblies, the fragmented assemblies do have more short proteins.

They just don’t have more than the PacBio complete assemblies.  Odd that.  If there were no uncorrected errors in the PacBio assemblies, they would be more like the Sanger assemblies than the Illumina ones.

Yersinia enterocolitica

Of the 176 GenBank genomes for this species, my automated script could only detect sequencing technology for 35 of them.  Here are the 21 that have a claim to be complete or near-complete (<5 contigs)

Accession Technology contigs # proteins # short
GCA_000834195.1 Illumina+454 2 4161 17
GCA_000987925.1 PacBio 2 4340 19
GCA_001304755.1 PacBio 2 4344 20
GCA_002082275.2 PacBio+Illumina 1 4067 31
GCA_002554625.2 PacBio+Illumina 1 4384 35
GCA_001305635.1 Illumina 2 4162 35
GCA_000834795.1 PacBio+Illumina 2 4259 36
GCA_000755045.1 Illumina+454 2 4226 44
GCA_000834735.1 PacBio+Illumina 2 4138 48
GCA_000755055.1 Illumina+454 1 4095 53
GCA_000754975.1 Illumina+454 2 4083 53
GCA_000597945.2 Illumina+454 3 4640 59
GCA_000754985.1 Illumina+454 3 4282 65
GCA_002083285.2 PacBio+Illumina 4 4198 76
GCA_002082245.2 PacBio+Illumina 2 4521 106
GCA_001708575.1 PacBio 3 4673 221
GCA_001708615.1 PacBio 3 4615 224
GCA_001708635.1 PacBio 3 4659 224
GCA_001708655.1 PacBio 3 4654 226
GCA_001708555.1 PacBio 3 4674 230
GCA_001708595.1 PacBio 2 4733 235

Slightly different story here, in that the PacBio (and PacBio hybrid) genomes appear to have some of the lowest number of predicted short proteins.  This is what people now expect when they see PacBio bacterial genomes.  However, there are also six PacBio genomes at the bottom of the table, and so I don’t think you can really look at this data and think there isn’t a problem.  It’s possible that those six just happen to be the strains of Yersinia enterocolitica that have undergone the most pseudogenisation, but I don’t think so.



Let’s get some things straight

  • I know this is an incomplete analysis and obviously more work needs to be done
  • If I personally wanted a perfect microbial genome, I would probably use PacBio+Illumina
  • I have nothing against PacBio
  • Nanopore aren’t in this list because they’re not in the species I chose, but I am sure they would also have significant problems

 

As I said above, it’s not that PacBio has a problem per se, it’s that people have a problem.  Yes, many errors are correctable with Quiver, Arrow and Pilon; often multiple rounds are necessary and you still won’t catch everything.

But not everyone knows that, and it’s clear to me from the above that many people are still pumping out poor quality, uncorrected, indel-ridden PacBio genomes.

The same is true for Nanopore, I have no doubt.

Let’s stop bullshitting.  These technologies have problems.  It doesn’t mean they are bad technologies, anything but – both PacBio and Nanopore have been transformational.  There is no need for bullshit.

“With great power comes great responsibility” – in this case, the responsibility is two-fold.  One, stop contaminating public databases with sh*t assemblies; and two, stop bullshitting that this isn’t a problem for your favourite technology.  That helps no-one.

 

Let’s keep saying it, and say it louder: REVIEWERS ARE UNPAID

The arguments over peer review and whether we are obliged to do it generally fall on two sides – either it is or isn’t an implicit part of your job.   Stephen Heard falls into the former group, arguing that there are many things which are implicitly part of our jobs as academics, and which don’t make it into our job description.

I agree wholeheartedly with Stephen that peer-reviewing is not in my job description.  In fact it is nowhere to be seen.  It’s not in my employment contract either, nor has it ever been in any of my lists of annual objectives, after 16 years in academia.  In fact, I don’t think it’s ever been discussed, either in annual appraisal meetings or in my annual meetings with the institute director.  It doesn’t make it on to my CV either.

Here is a key point: I could never write another peer review for the rest of my career and my career would not suffer.  Not one bit.

It is not part of my job and I am not paid to do it.

(for the record, I do peer reviews! For free!)

In an increasingly pressurised environment where the only factors that influence my career progression are papers published and grants won; with over 6500 e-mails in my inbox which I have lost control of; and with a to-do list I have no chance of ever finishing, prioritisation is essential.  The key for any task is to be important enough to get into the “action” zone on my to do list.  Does peer review manage that?  Occasionally, but not often.

Would it get there more often if I was paid to do it?  Absolutely.  Why?  Because I have bills to pay and a small family and every little helps.  I imagine this is even more true for post-docs and early career researchers.  Why should they do something for free, often for profit-making organisations, when it doesn’t affect their career prospects one tiny bit?  The answer is simple: they shouldn’t.

A common argument is this: if everyone stopped peer reviewing, science would grind to a halt.  Well unfortunately that ignores reality.  If delivery drivers stopped driving, would there be no food on the shelves?  No.  Because we wouldn’t and couldn’t let that happen.  We’d find whatever incentive needed to be found, and make sure the drivers still drove.  The same is true of peer review.  If you are struggling to find people, there is a simple solution, one that is as old as money itself: pay them.

(note: I do many peer reviews and I will continue to do so; free.  However, I believe it is time to re-think incentives, and yes, it is time to pay people for peer reviews)

It’s a bit POINTLESS if you forget the POINTLESS in POINTLESS ADMIN

Rather predictably, a Guardian article railing against pointless admin has stimulated a response from the university admin community.   Unfortunately, the response kind of misses the point – academics are annoyed at POINTLESS ADMIN, not at administrators in general (though the two are not entirely unrelated).

Here’s the thing – there is both pointless and essential administration, and at the same time, there are both excellent and poor administrators.  An attack on pointless admin is not an attack on good administrators.   We all can recognise groups of excellent administrators without whom the place would fall apart.  No-one is attacking them.

So what is pointless admin?  There is so much of it I don’t know where to start.  Perhaps the best example is the recording of academic outputs.  My University insists I put them in PURE; Wellcome Trust insist I have an ORCID account; and BBSRC insist I use ResearchFish.  You can accept the motivation for this whilst at the same time recognising that it is genuinely pointless replication of effort.  Academics are angry not because this happens once or twice, but because it happens all the time and it is increasing in frequency.

So what makes a good administrator?  Well, I have always said “A bad administrator reminds you to do something, a good administrator does it for you”.  There are caveats, but it’s a good starting point.  A quick guide for administrators might be something like this: “Is this a tick-box exercise?  Can you tick the box?  Then tick the box.  Please.  Thank you!   Does it really need the academic’s input?  Can they send bullet points and you do the rest?  Let’s do that then!  Otherwise are there any parts you can fill in?  I’d love for you to fill them in!  Is it possible to visit and not send yet another e-mail?  That would be awesome.  You can ask if a follow-up email would help and then send one afterwards.  Is there a possibility that one system/form can be filled in and then the same information copied to other systems/forms?  Can you do the copying?  Awesome!  And, as an aside, can we maybe have less systems/forms if they contain the same information?  Amazing”.

The obvious response to all of this is “why should the admins have to do all of that?  You arrogant ****!  Do your own admin!”.  This misses an unfortunate point – we are drowning.  If academia was a near-death experience, then academics are 200 yards off shore, in a rip-tide, barely breathing with our arms in the air, waving for help.   We need help.  Our job is to teach, to publish papers and to win research grants, research grants with overheads, all of which go some way to sustaining the very institution we all work for.   Every minute doing admin is a minute we are not doing the thing that keeps the lights on.

Please.  Help us.  Remove POINTLESS ADMIN.  And be a good administrator, not a bad one.

Judge rules in favour of Oxford Nanopore in patent dispute with PacBio

Forgive me if I get any of the details wrong, I am not a lawyer, but the title of this post is my take on a judgement passed down in the patent infringement case PacBio brought against ONT.

To get your hands on the documentation, you need to register and log in to EDIS, click “Advanced Search”, do a search for “single molecule sequencing” and click the top hit.

My interpretation of the documentation is that the judge has massively limited the scope of the patents in question by expanding on the definition of “single molecule sequencing”.  ONT argued that in the patents in question, “single molecule sequencing” referred only to “sequencing of a single molecule by template-dependent synthesis”, and the judge agreed with this definition.

sms

All claims are then subsequently limited to template-dependent synthesis, which of course is NOT what Oxford Nanopore do.

tds

The document then goes into an area that would make all biological ontologists rejoice – THEY TRY AND DEFINE THE TERM “SEQUENCE”.  I can almost hear the voices shouting “I told you so!” coming out of Manchester and Cambridge as I write 😉

HiSeq move over, here comes Nova! A first look at Illumina NovaSeq

Illumina have announced NovaSeq, an entirely new sequencing system that completely disrupts their existing HiSeq user-base.  In my opinion, if you have a HiSeq and you are NOT currently engaged in planning to migrate to NovaSeq, then you will be out of business in 1-2 years time.  It’s not quite the death knell for HiSeqs, but it’s pretty close and moving to NovaSeq over the next couple of years is now the only viable option if you see Illumina as an important part of your offering.

Illumina have done this before, it’s what they do, so no-one should be surprised.

The stats

I’ve taken the stats from the spec sheet linked above and produced the following.  If there are any mistakes let me know.

There are two machines – the NovaSeq 5000 and 6000 – and 4 flowcell types – S1, S2, S3 and S4.  The 6000 will run all four flowcell types and the 5000 will only run the first two.  Not all flowcell types are immediately available, with S4 scheduled for 2018 (See below)

S1 S2 S3 S4 2500 HO 4000 X
Reads per flowcell (billion) 1.6 3.3 6.6 10 2 2.8 3.44
Lanes per flowcell 2 2 4 4 8 8 8
Reads per lane (million) 800 1650 1650 2500 250 350 430
Throughput per lane (Gb) 240 495 495 750 62.5 105 129
Throughput per flowcell (Gb) 480 990 1980 3000 500 840 1032
Total Lanes 4 4 8 8 16 16 16
Total Flowcells 2 2 2 2 2 2 2
Run Throughput (Gb) 960 1980 3960 6000 1000 1680 2064
Run Time (days) 2-2.5 2-2.5 2-2.5 2-2.5 6 3.5 3

For X Ten, simply mutiply X figures by 10.  These are maximum figures, and assume maximum read lengths.

Read lengths available on NovaSeq 2×50, 2×100 and 2x150bp.  This is unfortunate as the sweet spot for RNA-Seq and exomes is 2x75bp.

As you can see from the stats, the massive innovation here is the cluster density, which has hugely increased. We also have shorter run times.

So what does this all mean?

Well let’s put this to bed straight away – HiSeq X installations are still viable.  This from an Illumina tech on Twitter:

 

We learn two things from this – first, that HiSeq X is still going to be cheaper for human genomes until S4 comes out, and S4 won’t be out until 2018.

So Illumina won’t sell any more HiSeq X, but current installations are still viable and still the cheapest way to sequence genomes.

I also have this from an un-named source:

speculation from Illumina rep “X’s will be king for awhile. Cost per GB on those will likely be adjusted to keep them competitive for a long time.”

So X is OK, for a while.

What about HiSeq 4000? Well to understand this, you need to understand 4000 and X.

The HiSeq 4000 and HiSeq X

First off, the HiSeq X IS NOT a human genome only machine.  It is a genome-only machine.  You have been able to do non-human genomes for about a year now.  Anything you like as long as it’s a whole genome and it’s 30X or above.  The 4000 is reserved for everything else because you cannot do exomes, RNA-Seq, ChIP-Seq etc on the HiSeq X.  HiSeq 4000 reagents are more expensive, which means that per-Gb every assay is more expensive than genome sequencing on Illumina.

However, no such restrictions exist on the NovaSeq – which means that every assay will now cost the same on NovaSeq.   This is what led me to say this on Twitter:

At Edinburgh Genomics, roughly speaking, we charge approx. 2x as much for a 4000 lane as we do for an X lane.  Therefore, per Gb, RNA-Seq is approx. twice as expensive as genome sequencing.  NovaSeq promises to make this per-Gb cost the same, so does that mean RNA-Seq will be half price?  Not quite.  Of course no-one does a whole lane of RNA-Seq, we multiplex multiple samples in one lane.  When you do this, library prep costs begin to dominate, and for most of my own RNA-Seq samples, library prep is about 50% of the per-sample cost, and 50% is sequencing.  NovaSeq promises to half the sequencing costs, which means the per-sample cost will come down by 25%.

These are really rough numbers, but they will do for now.  To be honest, I think this will make a huge difference to some facilities, but not for others.  Larger centers will absolutely need to grab that 25% reduction to remain competitive, but smaller, boutique facilities may be able to ignore it for a while.

Capital outlay

Expect to get pay $985k for a NovaSeq 6000 and $850k for a 5000.

Time issues

One supposedly big advantage is that NovaSeq takes 40 hours to run, compared to the existing 3 days for a HiSeq X.   Comparing like with like that’s 40 hours vs 72 hours.  This might be important in the clinical space, but not for much else.

Putting this in context, when you send your samples to a facility, they will be QC-ed first, then put in library prep queue, then put in sequencing queue, then QC-ed bioinformatically before finally being delivered.  Let’s be generous and say this takes 2 weeks.  Out of that sequencing time is 3 days.  So instead of waiting 14 days, you’re waiting 13 days.  Who cares?

Clinically having the answer 1 day earlier may be important, but let’s not forget, even on our £1M cluster, at scale the BWA+GATK pipeline itself takes 3 days.  So again you’re looking at 5 days vs 6 days.  Is that a massive advantage?  I’m not sure.  Of course you could buy one of the super-fast bioinformatics solutions, and maybe then the 40 hour run time will count.

Colours and quality

NovaSeq marks a switch from the traditional HiSeq 4 colour chemistry to the quicker NextSeq 2 colour chemistry.  As Brian Bushnell has noted on this blog, NextSeq data quality is quite a lot worse than HiSeq 2500, so we may see a dip in data quality, though Illumina claim 85% above Q30.

 

Is the long read sequencing war already over?

My enthusiasm for nanopore sequencing is well known; we have some awesome software for working with the datawe won a grant to support this work; and we successfully assembled a tricky bacterial genome.  This all led to Nick and I writing an editorial for Nature Methods.

So, clearly some bias towards ONT from me.

Having said all of that, when PacBio announced the Sequel, I was genuinely excited.   Why?  Well, revolutionary and wonderful as the MinION was at the time, we were getting ~100Mb runs.  Amazing technology, mobile sequencer, tri-corder, just incredible engineering – but 100Mb was never going to change the world.  Some uses, yes; but for other uses we need more data.  Enter Sequel.

However, it turns out Sequel isn’t really delivering on promises.  Rather than 10Gb runs, folk are getting between 3 and 5Gb from the Sequel:

At the same time, MinION has been coming along great guns:

Whilst we are right to be skeptical about ONT’s claims about their own sequencer, other people who use the MinION have backed up these claims and say they regularly get figures similar to this. If you don’t believe me, go get some of the World’s first Nanopore human data here.

PacBio also released some data for Sequel here.

So how do they stack up against one another?  I won’t deal with accuracy here, but we can look at #reads, read length and throughput.

To be clear, we are comparing “rel2-nanopore-wgs-216722908-FAB42316.fastq.gz” a fairly middling run from the NA12878 release, m54113_160913_184949.subreads.bam and one of the Sequel SMRT cell datasets released.

Read length histograms:

minion_vs_pacbio

As you can see, the longer reads are roughly equivalent in length, but MinION has far more reads at shorter read lengths.  I know the PacBio samples were size selected on Blue Pippin, but unsure about the MinION data.

The MinION dataset includes 466,325 reads, over twice as many as the Sequel dataset at 208,573 reads.

In terms of throughput, MinION again came out on top, with 2.4Gbases of data compared to just 2Gbases for the Sequel.

We can limit to reads >1000bp, and see a bit more detail:

gt1000minion_vs_pacbi

  • The MinION data has 326,466 reads greater than 1000bp summing to 2.37Gb.
  • The Sequel data has 192,718 reads greater than 1000bp, summing to 2Gb.

Finally, for reads over 10,000bp:

  • The MinION data has 84,803 reads greater than 10000bp summing to 1.36Gb.
  • The Sequel data has 83,771 reads greater than 10000bp, summing to 1.48Gb.

These are very interesting stats!


This is pretty bad news for PacBio.  If you add in the low cost of entry for MinION, and the £300k cost of the Sequel, the fact that MinION is performing as well as, if not better, than Sequel is incredible.  Both machines have a long way to go – PacBio will point to their roadmap, with longer reads scheduled and improvements in chemistry and flowcells.  In response, ONT will point to the incredible development path of MinION, increased sequencing speeds and bigger flowcells.  And then there is PromethION.

So is the war already over?   Not quite yet.  But PacBio are fighting for their lives.

From there to here

This is going to be quite a self-indulgent post – in summary, I am now a full Professor at the University of Edinburgh, and this is the story of my early life and career up until now.  Why would you want to read it? Well this is just some stuff I want to say, it’s a personal thing.  You might find it boring, or you may not.  There are some aspects of my career that are non-traditional, so perhaps that will be inspiring to others; to learn that there is another way and that there are multiple routes to academic success.

Anyway, let’s get it over with 😉

Early life

I was born and bred in Newcastle.  I come from a working class background (both of my grandfathers were coal miners) and growing up, most of my extended family lived in council houses.  I went to a fairly average comprehensive (i.e. state) school, which I pretty much hated.  Something to endure rather than enjoy.  Academic ability was not celebrated – I don’t know the exact figures but I’d guess less than 5% of my fellow pupils ended up in higher education.  Being able to fight and play football were what made you popular, and I could do neither 🙂 Choosing to work extra hours so I could learn German didn’t improve my popularity much…

My parents both worked hard – really hard – and I had everything I needed, but not everything I wanted.  Looking back this was a good thing.  My Dad especially is a bit of a hero.  He started off as a “painter and decorator” – going to other peoples’ houses and doing DIY, painting, putting up shelves, wallpaper, laying carpets etc.  As if doing that, having a small family (I have an older brother) and buying a house weren’t enough, he studied part-time for a degree in sociology at Newcastle polytechnic, famously going off to do painting and decorating jobs between lectures, and at the weekends.  After graduating, he went on to have a successful career in adult social care, and finished life as lecturer at a further education college.  My mother also worked in social care, and together they supported me through University (BSc and MSc).  Just amazing, hard working parents.  I attribute my own work ethic to both of them, they set the example and both my brother and I followed.

Education

I did a BSc hons in Biology at the University of York.  Some bits I loved, some bits I didn’t, and I came out with a 2.1.

One practical sticks in my mind – in pairs, we had 3 hours to write a program in BASIC (on a BBC B!) to recreate a graph (yes – we had to recreate an ASCII graph) based on an ecological formula (I don’t remember which).  I finished it in ten minutes and my partner didn’t even touch the keyboard.  Writing this now reminds me of two things – firstly, hours sat with my Mum patiently punching type-in programs into our Vic 20 so I could play space invaders (written in, you guessed it, BASIC); and secondly, hacking one of my favourite ZX Spectrum games, United, so I could have infinite money to spend on players.  Happy days!

At the end of my undergraduate, I didn’t know what else to do, so I took the MSc in Biological Computation, also at the University of York.  This was awesome and I loved every minute (previous graduates include Clive Brown, but more about that later).  The prospectus was so wide-ranging – we covered programming (in C), mathematical modelling, statistics (lots and lots of statistics), GIS and Bioinformatics, among many other courses.  It was hard work but wonderful.  It really taught me independence; that I could start the day knowing nothing, and end the day having completed major tasks, using nothing but books and the internet.

At the end of the course I had three job offers and offers to do a PhD – looking back this was a pivotal decision, but I didn’t realise it at the time.  I chose a job in the pharmaceutical industry.

Early career

My first job was a 12 month contract at GlaxoWellcome in Stevenage.  GW had invested pretty heavily in gene expression arrays.  Now, these were very different to modern microarrays – this was pre-genome, so we didn’t know how many genes were in the human genome, nor what they did.  What we had were cDNA libraries taken from various tissues and normalised in various ways.  These would be spotted on to nylon membranes, naively – we didn’t know what was on each spot.  We then performed experiments using radioactively labelled mRNA, and any differentially expressed spots were identified.  We could then go back to the original plate, pick the clone, sequence it and find out what it was.

It’s now obvious that having a genome is really, really useful 😉

I was in a team responsible for all aspects of the bioinformatics of this process.  We manufactured the arrays, so we wrote and managed the LIMS; and then we handled the resulting data, including statistical analysis.  I worked under Clive Brown (now CTO at Oxford Nanopore).  He asked me in interview whether I could code in Perl and I had never heard of it!  How times have changed…. he was very much into Perl in those days, and Microsoft – we wrote a lot of stuff in Visual Basic.  Yes – bioinformatics in Visual Basic.  It can be done…

I spent about four years there – working under Francesco Falciani for a time – then left to find new challenges.  I spent an uneventful year at Incyte Genomics working for Tim Cutts (now at Sanger) and David Townley (now at Illumina), before we were all unceremoniously made redundant.  With the genome being published, Incyte’s core business disappeared and they were shutting everything down.

Remember this when you discuss the lack of job security in academia – there is no job security in industry either.  The notion of job security disappeared with the baby boomers, I’m afraid.

I managed to get a job at Paradigm Therapeutics, also in Cambridge, a small spin-out focused on mouse knockouts and phenotyping.  I set up and ran a local Ensembl server (I think version 12) including the full genome annotation pipeline.  This was really my first experience of Linux sys/admin and running my own LAMP server.  It was fun and I enjoyed it, but again I stayed less than a year.  Having been made redundant from Incyte, my CV was on a few recruitment websites, and from there an agent spotted me and invited me to apply for my first senior role – Head of Bioinformatics at the Institute for Animal Health (now Pirbright).

Academia

So, my first job in academia.  It’s 2002.  I am 28.  I have never been in academia before.  I have no PhD.  I have never written a paper, nor written a grant (I naively asked if we got the opportunity to present our grant ideas in person in front of the committee).  I am a group leader/PI so I am expected to do both – I need to win money to build up a bioinformatics group.  What the institute needed was bioinformatics support; but they wanted me to win research grants to do it.

This job really was really, really tough, and I was hopelessly ill-equipped to do it.

My first grant application (to create and manage pathway genome databases for the major bacterial pathogens we worked on) was absolutely annihilated by one reviewer, who wrote a two page destruction of all of my arguments.  Other reviewers were OK, but this one killed it.  Disaster.  I figured out that no-one knew who I was, I needed a foot-print, a track record and I needed to publish (I’d still like to find out who that reviewer was….)

In 2005 I published my first paper, and in 2006 my second.  You’ll note I am the sole author on both.  Take from that what you will.  Meanwhile I was also supporting other PIs at the institute, carrying out data analyses, building collaborations, and these also led to papers; and so slowly but surely I began building my academic life.  I got involved in European networks such as EADGENE, which eventually funded a post-doc in my lab.  I won a BBSRC grant from the BEP-II initiative to investigate co-expression networks across animal gene expression studies; and I successfully applied for and won a PhD studentship via an internal competition.  With papers and money coming in, the institute agreed to provide me with a post-doc from their core support and hey presto, I was up and running.  I had a research group publishing papers, and providing support to the rest of the institute.  It only took me five or six years of hard work; good luck; and some excellent support from one of my managers, Fiona Tomley.  During my time at IAH I had 7 managers in 8 years; Fiona was the only good one, and she provided excellent support and advice I’ll never forget.

So what are the lessons here?  I think this was an awful job and had I known better I wouldn’t have taken it.  At the beginning there was little or no support, and I was expected to do things I had no chance of achieving.  However, I loved it, every minute of it.  I made some great friends, and we did some excellent work.  I forged collaborations that still exist today.  I worked really, really hard and it was quite stressful – at one point my dentist advised gum shields as I was grinding my teeth – but ultimately, through hard work and good luck, I did it.

It’s worth pointing out here that I believe this was only possible in bioinformatics.  My skills were in such short supply that a place like IAH had no choice but to take on an inexperienced kid with no PhD.   This couldn’t have happened in any other discipline, in my opinion.  It’s sad, because ultimately I showed that if you invest in youth they can and will make a success of it.  Being older, or having a PhD, is no guarantee of success; and being young and inexperienced is no guarantee of failure.

Roslin

And so, in 2010, to Roslin.  There was quite an exodus from IAH to Roslin as the former shrank and the latter grew.  I was lucky enough to be part of that exodus.  My role at Roslin was to build a research group and to help manage their sequencing facility, ARK-Genomics.  I certainly don’t claim all of the credit, but when I arrived ARK-Genomics had a single Illumina GAIIx and when we merged to form Edinburgh Genomics, we had three HiSeq 2000/2500.  We also had significantly better computing infrastructure, and I’m proud that we supported well over 200 academic publications.  My research is also going really well – we have, or have had, grants from TSB, BBSRC, and industry, and we’re publishing plenty of papers too.  The focus is on improved methods for understanding big sequencing datasets and how they can contribute to improved farm animal health and production.  Scientifically, we are tackling questions in gut microbiome and host-pathogen interactions.

Roslin is a great place to work and has been very supportive; the group enjoys a small amount of core support through which we help deliver Roslin’s core strategic programmes; and it is an incredibly rich, dynamic environment with over 70 research groups and over 100 PhD students.  You should come join us!

In 2015, I was awarded a PhD by research publication – “Bioinformatic analysis of genome-scale data reveals insights into host-pathogen interactions in farm animals” (I don’t think it’s online yet) – and in 2016 promoted to Personal chair in bioinformatics and computational biology.  Happy days!

A note on privilege

Clearly being a white male born in the UK has provided me with advantages that, in today’s society, are simply not available to others.  I want readers of this blog to know I am aware of this.  I wish we lived in a more equal society, and if you have suggestions about ways in which I could help make that happen, please do get in contact.

So what next?

More of the same – I love what I do, and am lucky to do it!  More specifically, I want to be a champion of bioinformatics as a science and as an area of research; I want to champion the young and early career researchers; I want to continue to train and mentor scientists entering or surviving in the crazy world of academia; and I want to keep pushing for open science.  Mostly, I want to keep being sarcastic on Twitter and pretending to be grumpy.

Cheers 🙂

 

Tips for PhD students and early-career researchers

As we enter October, here at Roslin it is the start of the academic year and many new PhD students begin.  We have over 100 PhD students here at any one time; it’s a very exciting and dynamic environment.  However, for some (many?) a PhD is one of the most stressful things that will ever happen to them (ed: interesting choice of language).   So how can we get round that?  Below are my tips for new PhD students.  Note my experience is in bio, so if you’re in another field, be aware of that.  Enjoy.

1. Lead

PhD projects, and PhD supervisors, come in all shapes and sizes, and work in many different ways.  For some, there will be a very detailed plan for the whole 3/4 years, with well defined objectives/chapters etc; others will be little more than a collection of ideas that may or may not work; and many will be between these two extremes.  Whichever project/supervisor you have, you the student are responsible for making it all happen.  This will be difficult for many; some people are not “natural born” leaders; and even those who are may not have had much chance to practice.  However, we have to recognize that a PhD is not a taught course; it is a project whereby a student learns how to carry out their own research, to investigate their own ideas, to plan and execute research.  That doesn’t happen if someone tells you what to do at every stage.  So, lead.  Take the lead.  This is your project – if you have ideas that go beyond what’s written in the original project plan, then you now have the opportunity to explore them.  Of course take advice; speak to your supervisor; speak to other experts; figure out whether your ideas are good or not;  do things by the book and be healthy and safe.  But if your ideas are good and they are worth exploring, get on and do it.  If there is a predefined plan, execute it.  Don’t wait; don’t ask; don’t sit nervously waiting for your supervisor to ask if there’s anything you want to explore – get on and do it.  Lead.

2. Read

Read the literature.  In a fast paced field such as genomics, papers will be out of date within ~2 years.  This means that to be on top of your game, you will have to read a lot of papers.  This is something you need to just bite the bullet and do.  Hopefully, if you’re in a field you love, this won’t be too arduous.  Combine with Twitter (see below) and news feeds so you can figure out which papers to prioritize.  As I have said before, you want to be the student sending a mail to your supervisor saying “hey have you seen this cool new paper?” rather than the student receiving those mails.  Take a coffee, a bunch of papers, go somewhere quiet and read them.

3. Write

Write.  For the love of all that is holy, write.  Learn to write quickly and well.  Science is not only pipettes, tubes, plates, labs and computers; it is about writing.  As a scientist it’s what I spend my time doing more than any other activity.  Grants, papers, reviews, reports, plans, emails etc etc.  Being asked to put together a coherent (referenced!) 3-page document in 24 hours is not unheard of; being asked to do the same for a “one pager” in a few hours is even more common.  Writing is so important.  I can’t emphasize this enough.  If you hate writing, then perhaps science isn’t for you; honestly, genuinely, I mean that.  Think about it.  Being a scientist means being a writer. If all the results are in, papers shouldn’t take months to write; posters should take no more than a few hours.

4. Engage

I am not the first to say this and I won’t be the last, so here it is again – science is a social activity. Engage with people. Talk to people. Go to meetings, conferences, workshops and be active in them. Talk to people about yourself and about your project, ask them what their interests are. Much of success is about luck, about being in the right place at the right time. Go out and talk to people about what you do. Don’t be shy, don’t think they aren’t interested. You might also consider blogging and social media. The more you are out there, the more people know about you and what you’re doing, the higher chance they might want to work with you.

5. Record

Keep a record of everything you do. In my group, we use a wiki; others use Github; obviously lab-based students have a lab-book (but this isn’t always sufficient!). It doesn’t matter what you use, the basic requirement is to keep a record of what you’ve done to such a standard that the work can easily be understood and repeated by someone else. This will help you in future, and it may very well serve as a record for protecting intellectual property.

6. Tweet

It’s just possible that if I had to name the single thing that has had the biggest impact on my career, that thing might be joining Twitter. I can say with great confidence that people on every continent know who I am and what I do. I’m not sure that would have been true going on just my scientific record alone. Twitter has enabled me to meet, and engage with, 1000s of wonderful people, scientific leaders in their field. Twitter is an online community of (mostly liberal) forward-thinking scientists. If you’re not on Twitter, you don’t get it; I was once a person who didn’t get Twitter, I actually joined just to drum up applications for a job I had advertised. However, it has been a transformational experience. Now – it’s hard. When you first join, you have no followers, and no-one is listening. You have to work hard to get followers, to get retweets, and it’ll take years to get 1000s of followers. But it’s worth it, I promise you!

7. Learn

Find out what skills are in demand and try and focus your research on those. Bioinformatics is a good example – learn Unix, learn to code and learn some stats. If you have those, you will always be employable and in demand. Try and look for trends – at the moment CRISPR is very hot, as is single-cell work – if you’re in the lab, can you integrate these into your project and therefore practice these techniques? Seriously, anyone can do DNA preps and PCR; find out the skills and techniques that are in demand and learn them, if you can.

8. Plan

I want my PhD students to have a thesis plan by 3 months. You don’t have to stick to it, but it’s good to have an idea. What are the results chapters? What are the likely papers? If you are a post-doc, then if you have 3 years, what are you going to do with them? If you’re a PI, again, plan – what questions? Which experiments? Papers? Where is this going? What will be your first grant and how do you get to the stage where you are ready to be funded? Plan.

9. Speak

At meetings, conferences, workshops. Submit abstracts and talk about your research. If you are not confident at public speaking, then practice until you are. Don’t submit poster abstracts, submit speaking abstracts. People remember amazing talks they have seen more than they remember amazing posters. It’s quite common, I find, for young scientists to default to posters as they don’t feel ready or willing to speak. You must get over this. I know it’s hard. I used to be nervous as hell before speaking at conferences. However, it has to be done and it has to be done well. Practice is key. Get out there, overcome your fears, and do it.

10. Realise

You have an amazing job and an amazing position. You get to push back the boundaries of human knowledge. That’s your job. You come in to work and by the end of the day we know more about the world we live in than we did before. It is an amazing, incredible, privileged position to be in. Yes it’s hard; yes there are barriers and it can be stressful. However, if you can get by those, and you have a good supportive team around you, then you have the most amazing job/position in the world. Enjoy it!

And I’ll leave it there. As always, I look forward to your comments!

Why you probably shouldn’t be happy at Stern’s recommendations for REF

If you are a British academic then you will be aware that Lord Stern published his recommendations for REF (the research excellence framework) this week.  REF is a thoroughly awful but necessary process.  Currently your academic career is distilled down to 4 publications and assessed every 4-5 years.  Papers are classified via some unknown system into 2*, 3* or 4* outputs and your value as an academic recorded appropriately.   Given that higher REF scores result in more money for Universities, your individual REF score has a very real impact on your value to your employer.  This has pros and cons as I will set out below.

Here are some of the recommendations and my thoughts:

  • Recommendation 1: All research active staff should be returned in the REF
  • Recommendation 2: Outputs should be submitted at Unit of Assessment level with a set average number per FTE but with flexibility for some faculty members to submit more and others less than the average.
  • What currently happens?  At the moment your employer decides whether your outputs make you “REF-able”.  In other words, if you don’t have 4 good outputs/publications, you won’t be submitted and you are REF-invisible
  • Stern recommendation: Stern recommends that all research-active staff be submitted and that the average number of outputs is 2.  However, there is a twist – the number of submissions per person can be between 0 and 6.  Therefore you may be submitted with zero outputs, which is perhaps even worse than being REF-invisible.  Given the formula for the number of expected outputs is 2*N (where N is the number of research-active staff), if a University has less than 2*N good impacts, there must surely be a pressure to transfer those with few outputs onto a teaching contract rather than a research contract.  And given the range of 0 to 6, I can see established Profs taking up all 6, with early career researchers being dumped or submitted with zero outputs.  So I’m not impressed by this one.

 

  • Recommendation 3: Outputs should not be portable.
  • What currently happens?  At the moment, an output stays with the individual.  So if I publish a Nature paper during a REF cycle and then move to another University, then my new employer gets the benefit, rather than my old employer.  This has resulted in REF-based recruitment, whereby individuals are recruited by Universities (often with high salaries and incentives) specifically because they have good REF outputs.
  • Stern recommendation: that outputs are not portable.  Specifically that publications remain with the employer present when they are accepted for publication.   It’s worth reading what the Stern report says here: “There is a problem in the current REF system associated with the demonstrable increase in the number of individuals being recruited from other institutions shortly before the census date. This has costs for the UK HEI system in terms of recruitment and retention”.   Read and re-read this sentence in context – high impact publications directly influence how much money a University gets from the government; yet here Stern argues that this shouldn’t be used for “recruitment and retention” of staff who produce those publications.  In other words current REF rules are pitched not as some sort of incentive to reward good performance, but as some kind of unnecessary cost that should be banished from the system.   Yes – read it again – potential staff rewards for good performance (“retention”) are quite clearly stated as a “cost” and as a “problem” to HEIs.
  • What the old REF rules did, in a very real way, is give power to the individual.  Publish some high impact papers and not only will other HEI’s offer you a job, but your existing employer might try and keep you, offering incentives such as pay rises and promotions.  What Stern is recommending is that power is taken from the individual and handed to the institution.  Once you publish, that’s it, they own the output.  No need to reward the individual anymore.
  • This also has the perverse outcome that an institution’s REF score shows how good they were not how good they are.  Take an extreme toy example – University A might have 100 amazing researchers between 2010 and 2014 and achieve an incredible REF score in 2015; yet they all may have left to go to University B.  How good is University A at research?  Well, not very good because all of their research-active staff left – yet they still have a really good REF score.

 

I don’t really have any major objections to the other recommendations; I think Stern has done a pretty good job on those.  However, I’m not at all happy with 1-3 above.   There are actually very few incentives for pay rises amongst UK academics, and REF was one of those incentives.  Stern wants to remove it.  You can see how healthy your University’s accounts are here (from here);  you will see that the vast majority (about 110 out of 120) UK universities generated an annual surplus last year, and the whole sector generated a surplus of £1.8Bn.   Yet somehow, incentives to promote, recruit and retain staff who are performing well is  a “cost” and a “problem”.  I also don’t think that the recommendations help ECRs as they could remain invisible to the entire process.

In conclusion, I don’t think the recommendations of Stern – or to give him his full title, Professor Lord Stern, Baron of Brentford, FRS, FBA – do anything positive for the individual researcher, they don’t provide much help for ECRs, and they hand power back to Universities.

 

 

Plot your own EU referendum poll results

Due to the unspeakable horror of the EU referendum, I have to find something to make me feel better.  This poll of polls usually does so, though it is way too close for comfort.

Anyway, I took their data and plotted it for myself.  Data and script are on github, and all you need is R.

Enjoy! #voteRemain

voteRemain

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