NGS all a dream, everyone has to go back to using Staden

CAMBRIDGE.  The wonderful world of second- and third- generation sequencers has all been a huge dream caused by a mass psychosis induced simultaneously in thousands of scientists because no-one at the Sanger Centre ever answered their e-mails, The ScienceWeb has learned.

The result is that everyone is going to have to go back to using Staden, staring intently at green, red, black and blue bumps and trying desperately to figure out if they mean anything.

But not everyone was sad at the news.  “Those were the days!” said Peter Curry, who announced plans to reform the HGMP at Hinxton.  “Back in the day when genomics was done by literally 100s of scientists sat in a big room staring at Staden all day.  Wonderful times.  Ahhhh, this is great news!”

“There have been clues!” said Rick Slowman of the Birmingham Institute.  “I mean, at the end there, we had a tiny USB-powered sequencer.  Of course that’s a dream, I mean, how could that be real?”

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Most bioinformaticians to be replaced by BEDTools

VIRGINIA.  Most bioinformaticians will be replaced by BEDTools over the next few years, The ScienceWeb has learned.

Throughout the world, institute directors are coming to the dawning realization that simply installing and running BEDTools will save them thousands of dollars compared to the cost of employing bioinformaticians.

BEDTools is a suite of software tools that tells you which things overlap other things in the genome, which is essentially what 95% of bioinformaticians spend their time doing.  Instead of using BEDTools to accomplish this task, however, most bioinformaticians hack 1000s of lines of pointless Python, Perl or Ruby to achieve the same thing.

Darren Quinnlon, author of BEDTools, said “As soon we wrote it, I knew we had killed the careers of the vast majority of chancers out there who claim to be doing bioinformatics.  I’m just surprised it has taken this long” he finished.

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Every biologist now an expert in precision medicine

LONDON, UK.  A recent survey carried out by The ScienceWeb has revealed that every single biologist in the world has now declared themselves an expert in precision medicine, even those who have never worked in human biology before.

“As soon as I saw that announcement from Obama, I knew I had to become an expert in precision medicine” said Dr Joey Batter from the University of the Bahamas.  “I didn’t even know what it meant, so I looked it up on Wikipedia.  And now I’m an expert.  It doesn’t matter that I’ve spent my entire career studying the mating rituals of the greater-spotted purple spider frog.  I’m into precision medicine now” she finished.

Not all are happy though.

“I’ve been saying that precision medicine is the future since 1984!” said Dick Spotson of the Roslin Institute.  “And it was, back then … and it’s still the future now!  I don’t know if I’m still right, or very, very wrong – it’s like groundhog day.  We called it  pharmacogenomics back then.  When is this f*cking future going to happen then, eh?” he finished angrily.

In other news, Ewingsworth Barney III (an expert in precision medicine) has been made co-lord-king-overseer at the EBI (Extra Bioinformatics Information).  Alf Rottweiler has been promoted to work alongside him in case anyone asks Ewingsworth a question about proteins.

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Each bioinformatician to have their own personal short-read aligner by 2016

OXFORD, UK.  The Bioinformatics Society (“BS” for short) have declared that they will reach their aim of every bioinformatician having their own personal short-read aligner by the end of 2016, The ScienceWeb have learned.

There are approximately 28,362 scientists globally who identify themselves as being “bioinformaticians” or “computational biologists” (those who identify themselves as “bioinformagicians” have been excluded – not just from this analysis, but from life in general).  A recent survey of short-read aligners identified 23,872 different software tools, all of which basically do the same thing.

“We’re almost there!” exclaimed base-pair hyper-bot Hang Li from the Broad Institute.  “As soon as I published that paper on the Ferris Bueller transform, I knew the field would take off!  And it has – we have one valuable publication and 23,871 incremental improvements” finished the Hang Li AI, a 7-dimensional intelligence that exists only in the minimal amount of memory need to represent a human.

The field of bioinformatics sequence analysis has been criticised by other areas of science for basically solving the same 3 problems over and over again, sometimes with only a marginal improvement and often with a marked deterioration in quality.

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REF was just a “massive practical joke” admits UK government

LONDON, UK.  The recent REF exercise, apparently an effort to assess the research excellence of UK universities, was all a “massive practical joke”, the UK government revealed today.

“I can’t believe anyone took it seriously” said Georgie Freeman, UK minister for the pointless.  “I mean, Universities are huge, mult-million-pound endeavours, full of thousands of academics from hundreds of different disciplines, each with rich and complex careers… and we said… we said… *snigger* … we said that we’d assess them all by asking for their four – FOUR?! – best papers from the last five years!  That’s funny right?  Do you get it? Eh?” he finished.

A spokesperson revealed that UK universities were less than impressed:   “We all knew that REF was bollocks, of course.  I mean how can buying in expensive academics at the last minute to boost our score possibly reflect our standing as a research-led university?  But to learn that it was all a joke?  That’s awful.  Are they insane?  We spent hundreds of millions of pounds on this!”

The office for business, entrepreneurship, skills and excellence (OBESE) has recently released new metrics that will be used to measure research excellence in 2018.  These include the number of likes on Facebook, the number of spurious, undefendable patents filed, the number and size of pointless spin-outs that never make any money, the sheer size of the admin department (with extra points for idiotic bureaucracy) and the number of times researchers sell-out to big business in order to get funding.

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All other languages tired of Python’s shit

New Zealand.  A recent survey of software languages has revealed that every single one of them is sick to the back teeth of Python telling them it’s better than everything else for everything.

Python, the most recent most popular programming language that will die in a few years time, has somehow managed to culture a following of developers who react to it with religious zeal.  Called Pythonistas within the Python religion, they are generally referred to as “pricks” by everyone else.

“It’s bullying, quite frankly” said Perl, a language once popular amongst developers.  “I basically can’t go out now.  As soon as I step outside of the house, a Pythonista/prick starts shouting in my ear about how shit I am.  It’s really disturbing”.

“I can’t believe they think they’re better than me at visualisation” said R.  “I mean, of course internally I am a mess, but my graphs are infinitely beautiful and you can just do so much more in me than you can do in Python.  And I don’t have problems with versions” R finished, sarcastically.

“Fuck Python, they don’t have Rails!” was all Ruby had to say, whilst a collective known as the C-mafia, representing C, C++ and C# just laughed in our faces when we mentioned Python as a serious programming language.

The ScienceWeb tried to call Java, but no-one was home.

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Glitch in The Matrix as NCBI goes down

BETHESDA. A glitch in The Matrix occurred earlier today as NCBI’s services briefly went down, serving to remind us all that we actually live in pods, asleep, existing only to provide energy to a super-race of hyper-intelligent aliens, known collectively as “The Bioinformaticians”.

The 20-minute downtime caused so much panic that some desperate scientists began suggesting everyone should switch to the EBI’s tools instead.  Luckily the NCBI came back up very quickly, as The Bioinformaticians noticed the glitch and removed it.

“Look, I don’t really care about an existential crisis based on the fact that this is all a drug-induced reality and that I am in fact about to have my kidneys harvested by space aliens” said Ed Smalls, a PhD student at MIT.  “But I’m half way through writing my thesis, don’t f*cking take away PubMed!” he finished.

The largest database at NCBI is of course the Short Read Archive, and whilst The Science Web tried in vain to find anyone who was actually using the database at the time, we were told that in fact no-one ever had.

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