Status Report: 2018: The light is at the end of the tunnel that I continue to build
Happy New Year! A long overdue update on whatever it is I am doing. Spoiler: It’s still a PhD.
Status Report: November 2016 (Part II): Revisiting the Synthetic Metahaplomes
The second installment of this year’s Christmas Special. We revisit our old friend, the DHFR dataset and discover that not everything is as awful as it seems.
bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes
Even `bowtie2`’s `–very-sensitive-local` option can be a little grumpy. Here’s how I make `bowtie2` a little more relaxed for alignment of more dissimilar sequences, particularly for my work on metagenomes.
Status Report: November 2016 (Part I): Triviomes, Treeviomes & Fuck Everything
It’s time for a PhD status report Christmas special. It’s a cliff-hanger episode, with a sad ending.
Bioinformatics is a disorganised disaster and I am too. So I made a shell.
I am not a very organised bioinformatician, and despite your best efforts, you probably aren’t either. I’ve written a tool called `chitin` that tries to keep me, and bioinformatics more organised.
Interdisciplinary talks and the metaphor-ome: Harder than metagenomics itself?
I gave a talk at Birmingham University. It was ok.
Jul Aug September 2016
A status update on the apparent progress of my doctorate, featuring a name for my work, and a brief run through all of the things that are and are not broken as of September 2016.
Status Report: May 2016 (Metahaplomes: The graph that isn’t)
Another long overdue insight to the things I am supposed to be doing so I can call myself a doctor someday.
Teaching children how to be a sequence aligner with Lego at Science Week
Every year, the university celebrates British Science Week with a Science Fair, inviting possibly the most difficult public to engage with: children. This year, I volunteered to run a stand.
Goldilocks: A tool for identifying genomic regions that are “just right”
I’m published! I’m a real scientist now! Check out the application note on Bioinformatics.