Opiniomics

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

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List of posts

  • Come and do a PhD with us!
  • Come and work with us
  • The three technologies bioinformaticians need to be using right now
  • Massive scale assembly of genomes from metagenomes in ruminants
  • Voice is dead, will email be far behind?
  • On stuck records and indel errors; or “stop publishing bad genomes”
  • How accurate is the nanopore-only assembly of GM12878?
  • With great power comes great responsibility
  • A simple test for uncorrected insertions and deletions (indels) in bacterial genomes
  • Let’s keep saying it, and say it louder: REVIEWERS ARE UNPAID
  • It’s a bit POINTLESS if you forget the POINTLESS in POINTLESS ADMIN
  • Judge rules in favour of Oxford Nanopore in patent dispute with PacBio
  • Beautiful boxplots in base R
  • HiSeq move over, here comes Nova! A first look at Illumina NovaSeq
  • University of California makes legal move against Roger Chen (and Genia)
  • Is the long read sequencing war already over?
  • People are wrong about sequencing costs on the internet again
  • Reading data from google sheets into R
  • From there to here
  • Tips for PhD students and early-career researchers
  • Creating an image of a matrix in R using image()
  • How to produce an animated gif of rise in global temperature in R
  • Plotting cool graphs in R
  • The unbearable madness of microbiome
  • Why you probably shouldn’t be happy at Stern’s recommendations for REF
  • Not providing feedback on rejected research proposals is a betrayal of PIs, especially early career researchers
  • I can’t recreate a graph from Ioannidis et al – can you?
  • Which reference manager do you use?
  • Plot your own EU referendum poll results
  • Open analysis of ZiBRA project MinION data
  • Converting from GenBank format to FASTA using Microsoft Excel
  • You don’t need to work 80 hours a week in academia…. but you do need to succeed
  • Your strongly correlated data is probably nonsense
  • Building a Kraken database with new FTP structure and no GI numbers
  • We need to stop making this simple f*cking mistake
  • Fast parallel access to data within MinION FAST5 files
  • Shots fired – nanopore wars part II
  • On preprints, open access and generational change
  • Did you notice the paradigm shift in DNA sequencing last week?
  • Doing the maths on PromethION throughput
  • Bioinformatics error responsible for retraction in Science
  • Dear NEJM…
  • The age of the dinosaurs is almost over; NEJM publishes one of their last dying roars
  • Which sequencer should you buy?
  • Travel tips for highly organised and important people
  • Online behavior, and an apology
  • Generate a single contig, hybrid assembly of E coli using MiSeq and MinION data
  • How to extract FASTQ from the new MinION FAST5 format using poRe
  • The five habits of bad bioinformaticians
  • We definitely do not need a “Steve Jobs” in biology
  • What I know about the expansion of HiSeq X to non-human genomes
  • What does the PacBio Sequel mean for the future of sequencing?
  • Extracting MinION fastq on the command line using poRe
  • Finally, a definition for bioinformatics
  • Why nanopore sequencing errors aren’t actually errors
  • Why I’m not jumping on the ORCID bandwagon
  • Assembling B fragilis from MinION and Illumina data
  • 4 predictions about nanopore sequencing in the next 12 months
  • Why FPKM makes sense
  • 101 bioinformatics facts
  • Complete Genomics Revolocity and the future of genome sequencing
  • Analysing MinION data with no bioinformatics expertise nor infrastructure
  • How journals could “add value”
  • On bioinformatics, and torturing the mechanic metaphor
  • Excited by bacterial DNA in sweet potatoes? Check this out!
  • On publishing software
  • Recreating a famous visualisation
  • You probably don’t understand heatmaps
  • The cost of sequencing is still going down
  • Defunding research excellence in Scotland
  • How to not sack your professors
  • How to recruit a good bioinformatician
  • Putting the HiSeq 4000 in context
  • Edinburgh and Glasgow invest in revolutionary HiSeq X clinical genomics technology
  • Easy and powerful graph editing using R and PowerPoint
  • 2014 in review
  • Ripping apart that terrible Atlantic piece on Open Access
  • A guide for running large projects
  • On Mars, Venus, Monkeys and Microbiomes
  • Proposal: identifying contaminated cancer cell lines
  • Why anonymous peer review is bad for science
  • Data from “The top 50 science stars of Twitter”
  • Thoughts on Oxford Nanopore’s MinION mobile DNA sequencer
  • poRe: an R package for the visualization and analysis of nanopore sequencing data
  • Citations are not a measure of quality
  • You’re not allowed bioinformatics anymore
  • How not to make your papers replicable
  • The lonely bioinformatician revisited: clinical labs
  • Comment on Piero Anversa controversy
  • We have the $1000 genome; what’s next?
  • An improved model for direct to consumer genome sequencing
  • How to stand out in academic scientific research
  • A Mothur tutorial: what can we find out about the horse gut metagenome?
  • Why do we do things?
  • Genomics: prepare for the quacks!
  • 4-year PhD funding for the development of exome sequencing in pigs
  • Biologists: this is why bioinformaticians hate you…
  • Is this a realistic portrait of a modern student/post-doc in biology?
  • The only core competency you’re ever going to need
  • Agreeing and disagreeing with a scientific legend

  • Welcome to the $1000 genome
  • On cheer-leading and pom-poms
  • The UK’s funding for open-access publications is not enough
  • Hypocrisy not limited to genomics
  • Thoughts on clinical genome sequencing
  • The de-democratization of sequencing
  • On Quilt Plots, and the need for editorial consistency
  • 7 reasons why the NextSeq 500 is a strange choice
  • Illumina destroy the opposition again – almost….
  • You’re probably not doing metagenomics
  • Cats, dogs and bioinformatics
  • The car park causation fallacy
  • Five things Randy Schekman should have done
  • I think you might be a hypocrite
  • HPC and biology; a marriage made in hell
  • We’re still recruiting!
  • A flow chart for feuding scientists
  • We didn’t ask for it
  • Nanopore wars
  • So you want to be a computational biologist?
  • Collection of published “guides” for bioinformaticians
  • We’re recruiting!
  • Genia single molecule sequencing
  • I think I might have something magical
  • How many hours have been wasted parsing unstructured text in biological databases?
  • Are you in peer review debt?
  • Should we sequence everyone at birth?
  • Food, fantasies and the future
  • Why I resigned as PLOS ONE academic editor
  • They Were Awful Titles
  • How wrong is David Moyes?
  • Piledriver in the Cloud
  • Bioinformatics is not something you are taught, it’s a way of life
  • Bacterial genomes – 2nd and 3rd generation costs
  • Five other foods that are like genome assembly
  • The KW metric
  • Assessing bioinformatics impact
  • Examples of the peer review system working
  • The $1000 myth
  • Traditional media – what’s to like?
  • Perhaps there is a chance to change something?
  • A quick guide to making your software installable
  • Celebrate the people who make your science possible
  • A pedantic look at the cost of sequencing
  • A guide for the lonely bioinformatician
  • Are you ready for the 20% cut in your sequencing budget?
  • Don’t tell me this isn’t how I’m supposed to be
  • Watson’s law of bioinformatics ontologies
  • The alternative “what it takes to be a bioinformatician”
  • Shouting at my data in the cloud
  • When was the last time you were wrong?
  • Dear ENCODE….
  • Researchers sequence ancient giant aquatic lizard thing
  • The reviewer’s oath
  • GATK – why it matters
  • Scientific Shakespeare
  • Ten things to consider when choosing an NGS supplier
  • Call the bioinformatics police!
  • Bacterial assembly on MiSeq – power of long reads?
  • An embargo on short read alignment tools

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Recent Posts

  • Come and do a PhD with us!
  • Come and work with us
  • The three technologies bioinformaticians need to be using right now
  • Massive scale assembly of genomes from metagenomes in ruminants
  • Voice is dead, will email be far behind?

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Recent Posts

  • Come and do a PhD with us!
  • Come and work with us
  • The three technologies bioinformaticians need to be using right now
  • Massive scale assembly of genomes from metagenomes in ruminants
  • Voice is dead, will email be far behind?

Meta

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January 2021
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 123
45678910
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