Monolithic pipelines are common in bioinformatics and particularly for metabarcoding. My view is that the word pipeline, and the type of software it refers to, may be holding us back and should be rethought. What is a pipeline? Pipelines are connected sets of programs, where information flows through the linked analysis algorithms as water flows…
metabarcoding numts
My PhD was hard. The grasshopper I was investigating (Chorthippus paralellus) had a huge number of mtDNA insertions into the nuclear chromosomal DNA (numt, pronounced ‘new-might’). PCR tended to amplify multiple templates. It was hard to get genuine mtDNA sequences. numts are known from almost all animals, though in most species they don’t get in…
Junk DNA deniers and Darwin Day
Is it is logically possible to accept the science of evolutionary biology and still deny the existence of junk DNA? I’m not sure. It is OK (though unfortunate) to be a biologist who is wrong in their assessment of an evolutionary topic. This is not a rejection of the mechanisms and rationale of evolution in…
10 things I’ve learned from teaching bioinformatics to students this semester
Jupyterhub works well for large classes Students can install everything they need from Github to Jupyterhub even when not command line savvy with git clone URL Jupyter notebooks work well as lab manuals, but notebooks would be much more useful if text formatting was better Google docs are better as lab manuals since I can edit…
What if conference talks were video preprints?
Conferences are about the rapid dissemination of new science to specialists in the same field. We should treat conference talks as we treat preprints, as a deliberate science dissemination process, and make video recording and proper archiving ubiquitous. Speaker-led demand Recording already happens of course, at some conferences, in a rough and ready way. My…
What are the frontiers in Open Science?
Many seem to misconstrue what ‘the frontier’ means in science, imagining a hard intellectual boundary, everything past which is unknown. I want to use a geographic frontier analogy that distinguishes the very limit (boundary) of human exploration (knowledge) from the area approaching that boundary. Frontier can mean both, but here I’m going to use it…
EvoPhylo blog
Here is the new location for my evophylo blog. Previously when I have an hour’s enthusiasm to write something, I’ve always been put off by the sheer hassle of dealing with my hosted WordPress site. It can take me an hour to log in. Its always broken. Then I try to tweet instead, which never…
Software and real carpentry
I like Software Carpentry, a non-profit organization teaching basic computing skills to researchers. But if I had one little criticism it would be that there wasn’t enough carpentry, with tenon saws, and mortising chisels, and rabbet planes. I like actual carpentry, I can’t tell you why, its a bit like asking why somebody likes cheese,…
Darwin the dropout
It annoys me slightly that almost all the pictures of Darwin circulating around on #DarwinDay are of some grey-haired old guy. Darwin made many of his important break-throughs as a young man. I mentioned ‘Darwin the dropout’ to my new class of evolution students this semester. Darwin was hassled by his dad to get a proper…
Tardigrade comparative genomics
There is now a second Tardigrade genome described in a manuscript (Koutsovoulos et al 2015), only days after the first (Boothby et al 2015– not OA). Koutsovoulos et al however strongly suggests that the widely publicised rampant horizontal gene transfer (HGT) is problematic. This alternate genome comes from Mark Blaxter’s group in Edinburgh, and has in fact…
EvoPhylo 