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Interestingly: the sentence adverbs of PubMed Central 16 Jul 2013 | 03:20 am
Scientific writing – by which I mean journal articles – is a strange business, full of arcane rules and conventions with origins that no-one remembers but to which everyone adheres. I’ve always been ...
“Open”: motivation versus definition 11 Jul 2013 | 03:00 am
Tweet length: 140 characters. Quote + URL that I wanted to tweet: 160 characters. Solution: brief blog post. the probability that people who can help each other can be connected has risen to the poin...
-omics in 2013 25 Jun 2013 | 10:51 am
Just how many (bad) -omics are there anyway? Let’s find out. 1. Get the raw data It would be nice if we could search PubMed for titles containing all -omics: However, we cannot since leading wildca...
No-one cares about your bioinformatics software 24 Jun 2013 | 02:36 am
Here’s a tip. When you write an article about your software, the title of which indicates that open-source is important: A universal open-source Electronic Laboratory Notebook but you then: provide...
Snippets: guts, cancers, statistics 18 Jun 2013 | 04:35 am
File under “interesting articles that I don’t have time to write about at length.” Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents Long ago, before metage...
Using the Ensembl Variant Effect Predictor with your 23andme data 4 Jun 2013 | 09:28 am
I subscribe to the Ensembl blog and found, in my feed reader this morning, a post which linked to the Variant Effect Predictor (VEP). The original blog post, strangely, has disappeared. Not to worry: ...
How to: bulk retrieval of archaeal genome sequences from the NCBI FTP site 28 May 2013 | 10:12 am
While we’re on the topic of mistaking Archaea for Bacteria, here’s an issue with the NCBI FTP site that has long annoyed me and one workaround. Warning: I threw this together minutes ago and it’s not ...
Oops: taxonomy #fail 28 May 2013 | 02:54 am
My journey from bench scientist to bioinformatician began with archaeal genomes. So I was somewhat startled to read The catalytic mechanism for aerobic formation of methane by bacteria, in which we le...
How to: remember that you once knew how to parse KEGG 22 Apr 2013 | 05:06 am
Recently, someone asked me if I could generate a list of genes associated with a particular pathway. Sure, I said and hacked together some rather nasty code in R which, given a KEGG pathway identifier...
A brief note: R 3.0.0 and bioinformatics 4 Apr 2013 | 03:07 am
Today marks the release of R 3.0.0. There will be plenty of commentary and useful information at sites such as R-bloggers (for example, Tal’s post). Version 3.0.0 is great news for bioinformaticians, ...
