London, UK. Due to the sheer lunacy of trying to sequence 100,000 people with only a few people and five laptops, Genomics England have decided to instead just impute from 1000 genomes data.
Jo Caulfield, comedienne and head of the project, told TheScienceWeb “It all seemed like such a good idea when I discussed it with David [Cameron]. 100,000 genomes, £100million, done. Brilliant. But then we thought about it… and it turns out that’s a lot of data, and, it turns out, analysing the data takes really big computers. We hadn’t really thought about that”
Tim Cupboard, who designed the informatics system, added “When I first spoke to Jo, he told me he had £100M to sequence 100,000 genomes. I mentioned that it was £1000 to sequence a genome, which would take up all of the budget, and did he have any money for staff and computers? He just looked at me blankly. So we scraped together enough money for 5 laptops and a few licences for CLC, but it turns out that’s not enough”
Instead, the team now intend to take out 100,000 23andMe subscriptions and then use 1000 genomes data to impute to whole-genome haplotypes. “It’s basically 85% accurate” said Tim, “surely that’s good enough for clinical practice?”
San Diego. Early adopters of the Illumina MiniSeq platform have reported that they are “absolutely delighted” that they are now capable of producing much shitter data than their University genomics facility, and at a far higher price.
Professor Stupid, one of the first to buy a MiniSeq, said “Well I had a bit of money left over in a grant that I needed to spend and now I have a beautiful MiniSeq! It’s wonderful! Shiny with flashing lights….”
At this stage Prof Stupid paused. Frowning, he continued “However, it turns out that you need someone who can actually create something called ‘a library’, and then someone who can analyse ‘data’. I hadn’t factored this in. Still, I have a student with a few years left on their PhD and we’ve been able to generate a few truly awful reads, so I am happy with our 4 months of work so far” he finished.
Dr Dumb, who works at a high profile University with one of the most successful genomics facilities in the US said: “I was fed up having to wait 6 weeks for my data. 6 weeks? Who do they think they are? So I got me a MiniSeq, and as long as I don’t count the cost of staff time, compute time and research overheads, we are almost as cheap as the facility! Plus I get my data in 4 weeks instead of 6 – well, that is as long as the damn thing works, which it never does – and well, we have nowhere to store the data so we’re spending $100s per run on USB hard disks – but it’s great. It really is”.
After interviewing Dr Dumb, we left the lab and couldn’t help but notice a NextSeq 500, covered in dust under a tarpaulin by the door.
Michigan, USA. The software carpentry foundation, who run the hugely popular “Software Carpentry” and “Data Carpentry” workshops, have announced a new range of workshops called “Software Dickery”.
Announcing the new range, Will Gregson had this to say: “What we noticed is that there are a lot of software engineers who act like complete dicks; and we thought: how do we teach the next generation to act like that? And hence Software Dickery was born”
C Brown Titan, one of the major advisors for the new workshops, continued “Software Dickery is all about teaching people how to be complete dicks – they need to get out there onto forums and start bullying n00bs, telling them to RTFM, stuff like that; they need to be getting into pointless arguments about which programming language is the best; and they need to be telling everyone who doesn’t use Jupyter how crap they are, and make them feel worthless”.
“We noticed this kind of behaviour was most prominent in the Python community, so Software Dickery will focus on Python to begin with” continued Brown Titan, a former member of Delta Force.
In the recent past, concerns have been raised about Python’s bullying of other languages, leading to an intervention by the G8.
LONDON, UK. Preprints, papers uploaded to the internet before they are peer reviewed, are definitely shit, according to a group of publishing companies who have a vested interest in seeing them fail.
“The problem with preprints, is, well they’re just shit aren’t they?” said a representative from Nurture Profits Group (NPG). “They haven’t got the sheen of quality that our career-editors and pompous reviewers add”.
When pushed for an example, she said “Preprints are too long, there are too many references, too many technical words, too much damn science. People don’t want to read that shit. What you need is a good editor to strip out 85-90% of the content, which goes in the supplement, and needlessly reduce the number of references. We also need to get all of those massive tables into PDF format, and insist on impossible, contradictory image specifications” she finished.
Academic publishers have been criticized recently for forcing researchers into unpaid slave labour, reviewing papers that they themselves have to pay to read, even after they have signed over copyright to their own content. It is a system so perfectly controlling and exploitative that even the Catholic church have praised it.
A guest post by Derek Blander, the most amazing scientist of all time….
In 1957, the world was bequeathed a gift – one of the greatest scientists to ever live was born – me. This post details some of my achievements since then, and I know you will all kneel down in front of me and worship my patents.
Despite being minus 4 years old, in 1953 I discovered the double helical structure of DNA. A few other people did a bit of minor ground work, such as Rosalind Franklin and Watson and Crick, but the most important bit was definitely me, no doubt about it.
In 1983, following many decades of hard work on my now beloved molecule, DNA, I invented the polymerase-chain reaction (PCR). This reaction can take a single molecule of DNA and amplify it many times over – one might say over-amplifying the achievements of that piece of DNA, something I have become incredibly good at.
In 1994 I turned to Maths and proved Fermat’s last theorum, then transferred careers to Scotland where my team cloned Dolly the sheep. I discovered the Tau neutrino in my spare time whilst single-handedly sequencing and publishing the human genome. Craig Venter is just a stray piece of my ego that broke away and became real.
I produced the first induced pluripotent stem cells, sequenced the neanderthal genome and discovered the Higgs boson whilst at CERN. Not only did I discover CRISPR, but I was actually the person who told God how to make it.
Now that we have the record straight, I hope you can all see just how amazing I am. You are lucky to know (of) me.
San Diego USA, the Poorly Assembled Genomes (PAG) meeting got off to an exciting start this year as a little know bioinformatics company ordasIT took centre stage having solved the age old ‘assembly problem’ with their new secret algorithm ‘DenovoHocusPocus’
Over the years scientists have been constantly frustrated by the fact that maths has stood in the way of getting a good assembly. Mike Devon, a Norfolk farmer and complex genomes specialist explained ‘we have been constantly told that genomes are fragmented because reads are short and repeats are long, therefore, because of something to do with maths, that biologists will never understand, we cant get long contigs just by sequencing more. It now turns out that the mistake we have been making has been that we have been over-thinking the problem”
Prof. Dumbledore, CEO of ordasIT and Head Wizard explained the DenovoHocusPocus methodology. “we observed that, historically, limitations imposed by physics have been overcome by using magic – so that’s the route we took here. However, people sometimes find the use of wizardry disturbing, so to help the end user we have made our entire assembly pipeline invisible”.
You cant run the ordasIT pipeline yourself as, to get around established mathematical theory, it must exist in a magical universe (a bit like Hogwarts). Instead you have to send your data to Dumbledore directly who, for a fee, will return a single contig per chromosome (or however many contigs you want).
Not all delegates at the PAG meeting were impressed, a sour faced delegate at the back of the room was overheard saying ‘this all smells like snake oil to me’, but nobody was listening and by that time Dumbledoor had left the building at high speed in his vintage Ferrari.
UK. Scientists revealed today that they are very surprised that Ash Dieback, a fatal fungal disease of ash trees, has maintained its relentless march through Europe, slaughtering millions of trees, despite their production of an online game designed to prevent the disease.
“It’s almost as if the fungus doesn’t have a Facebook account” lamented one of the authors.
“Gamification” is the process by which a complex problem may be solved by casting that problem as a game and allowing millions of online gamers to play for free, thus bringing huge crowd-sourced power to bear. It has been used to solve problems such as finding the optimum protein folding structure.
“The issue here ” said Mario ‘The Godfather’ Staccato “is that protein-folding is an abstract concept – it’s important, but knowing the answer doesn’t affect real life. Whereas ash dieback is a real fungus that attacks real trees in the real world and sticking a modified version of Tetris on Facebook realistically isn’t going to make any fucking difference” he finished.
The story of Fraxinus can be read at celebrity socialite scientist magazine eLife.