Sam Nicholls

My back of the envelope worst case calculation indicates 2.8 million decillion decillion possible valid paths so in retrospect, yes it was a bad idea to try and enumerate these to a terminal.

The Tolls of Bridge Building: Part IV, Mysterious Malformations

   Sam Nicholls    3 Comments    Sanger-QC

Following a short hiatus on the sample un-improvement job which may or may not have been halted by vr-pipe inadvertently knocking over a storage node at the Sanger Institute, our 837 non-33 jobs burst back in to life only to fall at the final hurdle of the first pipeline of the vr-pipe workflow. Despite my […]


   Sam Nicholls


   Sam Nicholls    2 Comments    Personal

On Sunday, I arrived in Leuven, Belgium, to begin my two month research visit at KU Leuven. Yes hello I am a Belgian now — Sam Nicholls (@samstudio8) August 2, 2015 Despite my 2pm ferry from Dover, with an aim to avoid or at least take into account the delays as a result of recent […]


The Tolls of Bridge Building: Part III, Sample (Un)Improvement

   Sam Nicholls    One Comment    Sanger-QC

Previously, on Samposium: I finally had the 870 lanelets required for the sample improvement process. But in this post, I explain how my deep-seated paranoia in the quality of my data just wasn’t enough to prevent what happened next. I submitted my 870 bridged BAMs to vr-pipe, happy to essentially be rid of having to […]

The Tolls of Bridge Building: Part II, Construction

   Sam Nicholls    One Comment    Sanger-QC

Last time on Samposium, I gave a more detailed look at the project I’m working on and an overview of what has been done so far. We have 870 lanelets to pre-process and improve into samples. In this post, I explain how the project has turned into a dangerous construction site. While trying to anticipate […]

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 […]