Mick W@tson ↙️
@BioMickWatson
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Bioinformatics | (meta) genomics | Data science. Some politics. Views are all my own and do not represent past, current or future employer.
Edinburgh
Joined December 2010
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Pinned Tweet
I have big news!
I will be leaving
@roslininstitute
and
@EdinburghUni
at the end of September to take up a new position as Principal Data Scientist at
@DSM
!
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Bioinformatics over the years:
1990s: doing a BLAST search
2000s: analysing 30 microarrays
2010s: nalysing 6Tb of NGS
2020s: creating a cloud the size of Netflix to reanalyse the whole of SRA for one figure
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Wow, that's one hell of a protein
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Hello this is your grants office. There is an unprecedented opportunity to bid for £30,000 of funding, but this has to be spent by next Tuesday. We're hoping to fund 1000 projects of £30 each. Attached is the 7 page form which must be submitted within 12 minutes of reading this
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@nilshomer
Visualise *everything*
Look at sequence reads, sequence assemblies, data, alignments, SNPs, PCA all of your numerical data.
Get into the *details* of your data
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PhD student: I hate writing
Post-doc: I hate writing, but I know I can do it
ECR: hey I'm pretty good at writing
Prof: the speed of bullshit from my hands, I am like superman
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Types of Bioinformatica paper
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Terrifying plot for those working in microbiome profiling
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As research committee season seems to be upon us again:
1) computational research is real research
2) no it doesn't take less time or effort than lab work
3) no you don't always need a hypothesis or specific biological question
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Still not over the fact RNA-Seq should have been called cDNA-Seq
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The three technologies bioinformaticians need to be using right now
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Your personal "R number" is how many people you have taught to use R
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Amusing conversation over lunch.
Academia:
you ask for 24 muffins
the funder gives you 20 muffins, and congratulates you on your 24 new muffins
Your university takes 10 muffins
You can't eat any muffins until legal say so, at a cost of 2 muffins
1/2
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So you want to learn BIOINFORMATICS?
Here are the top 5 tools that every elite bioinformatician uses every single day:
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Scientists for the last 50 years: there's going to be a global pandemic virus jump from animals
Public: ooooh did Dean Koontz predict COVID-19???!!!
Scientists: ... but ....
Public: my GOD how did Koontz know??!
Fever dreams: did author Dean Koontz really predict coronavirus?
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A tricky thing in science is to learn to always doubt your results, but never doubt yourself.
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Things people don't warn you about parenthood:
1) you will be permanently ill for at least 5 years
2) crying babies are not upset or sad, they are absolutely furious
3) you can take them to the most amazing places, but their favourite part of the day will be the ice cream
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Annual reminder that .docx and .xlsx files are zip files. Change the extension to .zip and take a look inside :)
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Delighted and honoured this morning to be confirmed as Head of Division for Genetics and Genomics
@roslininstitute
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Scientists inbox:
50% fake conference invites
30% fake journal invites
15% admin
3% questions from post docs they could answer themselves using google
1% "can you retweet my job advert?"
0.9% unavoidable meeting invites
0.1% science I'm interested in
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Idea: when you retire, don't become an emeritus professor to "finish all your projects".
Instead, coach an early career researcher in your field, hand over your expertise and ideas and go do the gardening.
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"Thanks for analysing our data. We'll add you to the acknowledgements section"
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Just gave my name in Starbucks as "BLAST is almost never the right tool" and when the barista called my name 100 angry biologists turned up and ripped my legs off
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1. New technology
2. "Oh my god it works" papers
3. "We need special tools" papers
4. "These are the best tools" papers
5. "A Bayesian approach to..." papers
6. Fight on StackExchange
7. Anonymous post on pubpeer
8. "Oh my god it's crap!" papers
9. "Microbiome"
Repeat
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Hey. So I got promoted.
Full Prof.
"Personal Chair in Bioinformatics and Computational Biology"
:-D
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New to bioinformatics? The main thing to remember is nothing has been written before, so remember to write everything from scratch in your favourite language 👍
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I'll get pushback for this, but if you don't recognise that Excel is an incredible piece of software that has some incredible features that we all could use, then you're wrong and perhaps not as objective about things as you think you are.
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Brilliant
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"If you educate people they won't vote tory!"
The Left will continue its resurgence so long as too many go to university
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Looking forward to all of the coronavirus papers to be publish in Nature, Science etc rediscovering stuff published in the J Poultry Science in 1992
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Publishing a bioinformatics tool with your own simulated data
A square wheel can roll smoothly only if the ground consists of evenly shaped inverted catenaries of the right size and curvature [The square-wheeled tricycle at the National Museum of Mathematics in New York City. Full video: ]
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#newPI
announcements
Everywhere: excited to start my new lab, I'm hiring multiple post-docs and students, hit me up!
UK: excited to start my new lab! I've got £500, where do people buy cheap paperclips?
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When you have two papers published in one day but get no social media attention because some plank claims to have CRISPR-ed a baby
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I see Excel is being hated on again. To be honest, its quick visual sorting, filtering and graphing functions are exceptional. Fantastic for initial exploration of the data. I use it daily.
Once I see the data, of course
#rstats
for serious graphs :)
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Not sure why people find parenting and academia hard. Here's a tip: simply split your time:
50% work
40% childcare
20% housework
20% cooking and meal prep
20% leisure time
10% family engagement
And don't forget to get 8 hours sleep!
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# of papers using single cell techniques: 10,000
# of papers describing novel bioinformatics technique on single cell data: 1,000,000,000,000
(approximate numbers)
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I first joined academia when I was 28. I had no PhD, I had never written a paper nor a grant, and now it was a fundamental part of my job.
I was terrified. Utterly frozen by the enormity of having to do something I had no idea how to do. 1/n
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16S RIGHT TOTALLY TRANSFORMATIVE TECHNOLOGY BUT THE UNIVERSAL PRIMERS AREN'T UNIVERSAL AND YOUR CHOICE OF V REGION REALLY MATTERS AND ALL THE DATABASES ARE WRONG AND THERE'S LOADS OF ERRORS IN THE DATA WHICH INFLATES YOUR OTU COUNT AND THERE'S A MASSIVE DEBATE ABOUT ASVs...
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Signing the professorial roll at Edinburgh's old college today.
Not bad for a coal miner's grandson.
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Your DNA is contaminated
Your genome is contaminated
Your microbiome is contaminated
Your reagents are contaminated
The databases are contaminated
PRINT THIS OUT and give it to your students and post-docs
Assembled a protozoan genome from cattle rumen.
Largest contig top BLAST hit is Sphaeramia orbicularis - common name Orbiculate cardinalfish.
I guess fish have protozoa in their microbiomes too :)
Unpopular opinion - this is why genome assembly should be left to experts
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As more and more people sequence genomes, we will eventually sequence the common ancestor of all life on earth and it will be PhiX and freaking illumina adapters
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Mindfulness for bioinformatics
- only use one core
- don't run jobs simultaneously
- let your job run "in the moment"
- clear your mind whilst the server does the work
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Bioinformatics is having to re-run your whole pipeline because some (essential) tool at the end has an undocumented requirement not to have dots in the filename
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This tweet can predict the impact of your research with 90% accuracy.
Are you ready?
Your research has no impact.
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Finance team set you up with a budget with 4 muffins in it
For the next decade, you have to submit a report on what you did with those 24 muffins
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I am thinking of forking the entire R codebase and changing "color" to "colour"
Who's with me?
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SEE EVERYONE GOES ON ABOUT LONG READS MAKING BETTER MAGS BUT REALLY IT'S ALL ABOUT DNA EXTRACTION AND YOU CAN'T GET LONG DNA FROM BEAD BEATING AND IF YOU DON'T BEAD BEAT HARD ENOUGH YOU BIAS THE SAMPLE AND IF YOU SIZE SELECT YOU BIAS THE SAMPLE AND U WON'T HAVE ENOUGH DNA
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"This isn't a research paper, it's a massacre"
TL;DR GWAS on uk biobank kills over 400 candidate gene studies
How would I know if my own research area was this wrong?
Our usual safeguards won’t save us: peer review, meta-analysis, 100s of conceptual replications, listening to eminent researchers. All failed.
This should be keeping us up at night.
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OK,
#protip
you might hate.
Microsoft Word can open PDFs.
Yes it can. File -> Open -> Choose PDF -> confirm conversion
PDFs can then be edited and saved as PDF or doc(x).
It can open PDF tables.
PDF tables can be copied and pasted into Excel.
Excel can save csv, tsv etc
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This is huge if it holds up. Epstein Barr virus triggers up to 7 auto immune diseases.
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Just found out my new PhD student has *mandatory* MATLAB training
Mandatory. MATLAB. Training.
For clarity, MATLAB will not be useful to her.
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"Microbes could be used..."
*rolls dice*
"... to capture carbon..."
*rolls dice*
"...on the international space station"
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Twitter laid me off today. If you know of any open positions for project managers or senior software engineers, let me know. I was in charge of the feature that made sure every bioinformatics debate descended into an argument about Python vs R.
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Amazing to see a software library published in NATURE!!!
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It's finally here! Our new paper in Nature Methods:
A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination | Nature Methods
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Can confirm that you can work your way all the way up to professor of bioinformatics, head of department, a 20 year career, and your collaborators will still ask you to upload the reads to ENA
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Paper accepted in principle in Nature Communications :-D
Time to open the champagne!
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2020 science predictions:
- Illumina will give up their pursuit of PacBio. PacBio will eventually fold and Illumina will buy the technology anyway (probably 2021).
- Nanopore will overtake Illumina in terms of cost-per-gb and PacBio in terms of quality
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That feeling when you realise "the block chain" is just a massive excel spreadsheet that people keep saving with a new name every time they edit it
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So, big news. We've been doing a massive comparison of short read aligners in terms of accuracy and speed. The results are surprising! We now recommend you change all your pipelines to use NCBI BLAST 👍
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If you're working in 16S microbiome research, please read our paper which tries to suggest best practices!
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1. SNP MP fondled two 17yr old girls behind his wife's back
2. SNP MSP de-frauded a pro-indy group
3. SNP MSP immorally flipped houses for a profit
4. Former SNP first minister accused of bullying
5. Current SNP first minister accused of cover up
But yeah sure, you're "better"
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Proposal: any additional experiments suggested by reviewers should be funded by those reviewers
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Universities: we want spin outs!
Scientists: sure we've got ideas....
Universities: great! You'll have to work 60-80 hour weeks, generate all your own investment, never see your family, and we will take a massive cut of all profits
Scientists: ummmm.... no
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So, just to be clear, the University mandatory travel agent:
1) gets the same flight prices we do
2) uses the same websites we do
3) won't choose seats or meals
4) costs us money
Have I got that right?
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The incredible cake my group got me
I have big news!
I will be leaving
@roslininstitute
and
@EdinburghUni
at the end of September to take up a new position as Principal Data Scientist at
@DSM
!
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Installing QIIME
After 53 attempts, Freestyle skier Andri Ragettli completes complex parkour course in Switzerland
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Postdoc and student persuading PI to submit to bioRxiv
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Proposal: a new journal aimed at publishing short responses to research articles
Call it "Scientific Retorts"
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Bioinformatician's log, stardate 2157.
We have colonized Mars, after Trump III's nuclear war with the EU-Korean alliance vaporized the Earth's atmosphere.
We have with us the nanopore device for detecting Martian microbes.... but... we still can't f*cking install QIIME
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Or: when bioinformaticians do all of the hard work but don't make it on to the paper
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Author of BEDtools builds a bed using tools.
You're welcome!
I took a needed break this PM to work on a swing bed for our backyard. Many mistakes to fix and much more to do,but I am looking forward to a nap this weekend.
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Bioinformatics is converting between file formats
Academia is just downloading PDFs that you’ll never read
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So Google now have the best variant caller and the best protein folding algorithm.
Really hope they don't get into metagenomics 😬
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Delighted that our latest rumen metagenomics paper is out in
@NatureBiotech
Almost 5000 high quality rumen MAGs, and three complete chromosomes using
@nanopore
data
Funded by
@BBSRC
and
@roslininstitute
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Amazing. We have discovered a method to create complete microbial assemblies using ILLUMINA metagenomics data, no need for long reads, perfect circular genomes every time. We call it Super Assembly MAGS, or SUPERASSMAGS for short. Preprint out soon!
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My unshakeable opinion:
All bioinformatics formats should transition to TSV / tabular
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Lab scientists! Bioinformaticians really suffer in the heat, please remember to leave out a bowl of RAM and some spare cores to help us cope
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