The Tolls of Bridge Building: Part I, Background

   Sam Nicholls    No Comments yet    Sanger-QC

I’m at the Sanger Institute for just another two weeks before the next stop of my Summer Research Tour and it’s about time I checked in. For those of you who still thought I was in Aberystwyth working on my tan1 I suggest you catch up with my previous post. The flagship part of my […]

Secure your Six

   Sam Nicholls    No Comments yet    Mysteries

As a financially constrained student, like many others, I use apache‘s support for Server Name Indication (SNI) to serve multiple SSL domains from one IP. I’m somewhat competent and the setup seems to work for all of my domains. Yet, some time ago I tried to access one of my VirtualHosts from work over SSL […]


   Sam Nicholls

Just when I think I have tricked the computer into finally doing what I want, it reveals that it has come up with a new way to fail obscurely and avoid detection.

Sanger Sequel

   Sam Nicholls    No Comments yet    Sanger-QC

In a change to scheduled programming, days after touching down from my holiday (which needs a post of its own) I moved1 to spend the next few weeks back at the Wellcome Trust Sanger Institute in Cambridgeshire. I interned here previously in 2012 and it’s still like working at a science-orientated Google thanks to the […]

When `True` is not `True`

   Sam Nicholls    No Comments yet    Mysteries

Today, whilst continuing development on Goldilocks, I discovered a minor oddity that left me a little confused and bemused before lunch: True did not appear to be True… Part of Goldilocks‘ functionality allows for the filtering of results; users may specify a dictionary of criteria whose keys map to functions to be applied to result […]

`rapsearch` Returns

   Sam Nicholls    No Comments yet    AU-PhD

Following completion of my most recent side-quest to find a little more about who the protozoa actually are and where they live in the context of UniProt, I now had a starting point to append to my archive of hydrolase records. I had already shown that around 1,500 Ciliophora-associated hydrolases could be extracted from UniProt, […]

Playing Phylogenetic Hide and Seek with Protozoa

   Sam Nicholls    No Comments yet    Bioinformatics, Mysteries

Amanda suggested that alongside archaeal, bacterial and fungal associated hydrolases, we should also look at protozoans. No problem, I’ll just get the taxonomy ID for protozoa and extract another database from UniProtKB as before. Simple! Or so I thought… The rabbit hole is pretty deep on this one. Feel free to skip my multi-day exploration […]


   Sam Nicholls    No Comments yet    Gadgets, Photography

The basement of the “old” biology building on campus is lined with beautiful microscopy images which I’d always been curious about. A few weeks ago I contacted the team responsible who were kind enough to offer some of their time to show their laboratory and demonstrate some of the processes involved. The team also extended […]

Raiding `rapsearch` Results

   Sam Nicholls    No Comments yet    AU-PhD

Finally. After all the trouble I’ve had trying to scale BLAST, running out of disk space, database accounting irregularities and investigating an archive_exception, we have data. Thanks to the incredible speed of rapsearch, what I’ve been trying to accomplish over the past few months with BLAST has been done in mere hours without the hassle […]