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,…

Frictionless reproducibility in phylogenomic experiments

This is a guest post by Amir Szitenberg, postdoctoral researcher in my group at the¬†University of Hull, and main author of @ReproPhylo I find the ReproPhylo approach to experimental phylogenomics very exciting, and can see how it would lead to better, in depth understanding of phylogenomic datasets, regardless of their size. An example for this…

ReproPhylo: a reproducible phylogenomics environment

Our new phylogenomics environment is called ReproPhylo. It makes experimental reproducibility frictionless, occurring quietly in the background while you work on the science. The environment has a lot of tools to allow exploration of phylogenomics data and to create phylogenomic analysis pipelines. It is distributed in a Docker container simplifying installation and allowing the reproducibility…

Reproducible phylogenetics part 3; how

tl;dr Phylogenetic experiments need explicitly designed reproducibility, rather than accidental or partial reproducibility. There are many working reproducibility solutions out there differing in their approach, interface and functions. There is no perfect solution for all cases, and you can learn a lot by investigating. Here I discuss a few software approaches to reproducible phylogenetics. I’m…

How can we ensure the persistence of analysis software?

I’ve been thinking about sustainable and accessible archiving of bioinformatics software, I’m pretty scandalized at the current state of affairs, and had a bit of a complain about it¬†before. I thought I’d post some links to other people’s ideas and talk a bit about the situation and action that is needed right now. Casey Bergman…

Bio-Linux in a VirtualBox

For those of you who haven’t come across it before Bio-Linux is an operating system set up for bioinformatics with a huge number of programs pre-installed. It can be obtained (for free) from the NERC Environmental Bioinformatics Centre. I’ve spent quite a while recently messing with installations of software packages and wanted to see how…

Droppable applications from scripts

I’m not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I’ve put together though. Sometimes when I need to run a script many times I’ve found the most irritating thing is launching the scripts and pointing…