Category: Mysteries

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 […]


  

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 […]


  

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 […]


TrEMBLing

   Sam Nicholls    No Comments yet    Bioinformatics, Mysteries

Something appears amiss with TrEMBL, millions of sequences are “missing”. Where did they go? At the end of last month, to build a database of bacterial sequences with known hydrolase activity1, I extracted around 2.9 million sequences from UniProtKB/TrEMBL; a popular database which contains sequences that have been automatically annotated and are awaiting manual curation […]