Extending ngless and interacting with other projects [4/5]

NOTE: As of Apr 2016, ngless is available only as a pre-release to allow for testing of early versions by fellow scientists and to discusss ideas. We do not consider it /released/ and do not recommend use in production as some functionality is still in testing. Please get in touch if you are interested in … Continue reading Extending ngless and interacting with other projects [4/5]

New Paper: Microbial abundance, activity and population genomic profiling with mOTUs2

Fresh off the press in Nature Communications, an update on the mOTUs (marker gene-based operational taxonomic units) concept. Basic summary of the motus concept This concept was introduced in the first mOTUs paper, which itself built upon the specI concept: Use single-copy marker genes to identify and quantify species in metagenomic samples. Single-copy marker genes are gene families such that (1) … Continue reading New Paper: Microbial abundance, activity and population genomic profiling with mOTUs2

NIXML: nix + YAML for easy reproducible environments

The rise and fall of bioconda A year ago, I remember a conversation which went basically like this: Them: So, to distribute my package, what do you think I should use? Me: You should use bioconda. Them: OK, that’s interesting, but what about …? Me: No, you should use bioconda. Them: I will definitely look … Continue reading NIXML: nix + YAML for easy reproducible environments

Using Gehan’s Test for Microbiome Longitudinal Studies

One of the nice things about blogging about my work is that I can use the blog to dig deep into a technical aspect that may would otherwise be buried in a little note in the Methods section. This is exactly such a post. In our recent paper on the dog microbiome (see previous blog summary), … Continue reading Using Gehan’s Test for Microbiome Longitudinal Studies

The Scientific Paper of the Future is Probably a PDF

I do not mean to say the scientific paper of the future should be a PDF, I just mean that it will mostly likely be a PDF or some PDF-derived format. By future, I mean around 2040 (so, in 20-25 years). I just read James Somers in the Atlantic, arguing that The Scientific Paper Is Obsolete (Here’s what’s next). … Continue reading The Scientific Paper of the Future is Probably a PDF