This is a guest post by Amir Szitenberg, a postdoc in my lab @EvoHull, describing a phylogenomic investigation using ReproPhylo. Amir used to be a sponge researcher if you can't tell from the tone below. Despite already knowing ReproPhylo could do all this rapidly and of course reproducibly, I...
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...
I've recently come across the idea of stars for open data quality thanks to Steve Moss. The table below is from 5stardata: ★ make your stuff available on the Web (whatever format) under an open license ★★ make it available as structured data (e.g., Excel instead of image scan...
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...
Previously I wrote about (1) why we need reproducibility in phylogenetics, (2) what we need to achieve it. This is part 2b, still writing about what we need to achieve reproducibility. My conclusion before was: "that most of the issues surrounding reproducible phylogenetics are solved problems...
In part 1 of this series I wrote about why we need reproducible phylogenetics, here I write about what we actually need to do. tl;dr We need only a few classes of things (open reusable archiving of all data, information provenance, recording of data treatments & software environments),...
We are still largely missing the benefits of reproducibility in phylogenetics. I think that this makes our lives unnecessarily difficult and makes us particularly poorly prepared to confront modern data-rich phylogenetics. In this first post "Why" I want to talk about why we need reproducible...
I received an email from Alex Lang and he asked about my current use of Electronic Lab Notebooks Hi Dave, I'm a physics graduate student who just started using a WordPress based ELN. I really found your thoughts on ELNs helpful, especially: http://www.davelunt.net/evophylo/2009/03/wordpress-as-eln/ https://speakerdeck.com/davelunt/electronic-lab-notebooks-for-ug-students Since someday I want to be...
I’m pretty proud of some parts of my workflow: electronic lab notebook, reproducibility, open data files, (semi-obsessive) automated data backups etc etc. But pride often comes before a fall. I had a bad experience this week where I thought I had lost some important phylogenetic...
