Category: AU-PhD

`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, […]


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 […]


What am I doing?

   Sam Nicholls    No Comments yet    AU-PhD

A week ago I had a progress meeting with Amanda and Wayne, who make up the supervisory team for the computational face of my project. I talked about how computers are terrible and where the project is heading. As Wayne had been away from meetings for a few weeks, I began with a roundup of […]


The Story so Far: Part I, A Toy Dataset

   Sam Nicholls    No Comments yet    AU-PhD

In this somewhat long and long overdue post; I’ll attempt to explain the work done so far and an overview of the many issues encountered along the way and an insight in to why doing science is much harder than it ought to be. This post got a little longer than anticipated, so I’ve sharded […]


Exit codes, core dumps, `set -e` and `expr`

   Sam Nicholls    One Comment    AU-PhD

The kernels on our cluster clients have recently been updated after I inadvertently stumbled across an old1 kernel bug that caused erratic behaviour when NFS tries to open a directory containing many files that are being written to simultaneously (more on which is another post in itself really, as usual). The update seems to have […]


  

First Post

   Sam Nicholls    No Comments yet    AU-PhD

Having spent quite some time ruminating over the contents of this inaugural blog post to a point beyond that of analysis paralysis, I have managed to avoid writing entirely. Thus I’ll remove this pedestal of preclusion and begin with an uninspiringly titled First Post. Hello, I’m Sam Nicholls; one of the latest PhD students to […]