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...
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...
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...
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...
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...
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...
