Comments for Samposium

Comment on Belgian by Status Report: May 2016 (Metahaplomes: The graph that isn’t) – Samposium

Sun, 12 Jun 2016 20:21:59 +0000

[…] the end of my first year, I returned from my reconnaissance mission to extract data mining knowledge from a leading Belgian university with a prototype for a data structure that was fit to house a metahaplome; a probabilistically […]

Comment on Status Report: February 2016 by Status Report: May 2016 (Metahaplomes: The graph that isn’t) – Samposium

Sun, 12 Jun 2016 20:03:28 +0000

[…] would seem that a sufficient amount of time has passed since my previous report to discuss how everything has broken in the meantime. You would have left off with a version of me […]

Comment on Wrangling WordPress by Using fail2ban to mitigate simple DOS attacks against apache – Samposium

Using fail2ban to mitigate simple DOS attacks against apache – Samposium — Tue, 07 Jun 2016 15:07:47 +0000

[…] I wanted to tie this into fail2ban, the daemon I use to block access to ssh, the mail servers, WordPress administration, and such. I found a widely distributed jail configuration for this purpose online but it did not […]

Comment on Belgian by Status Report: February 2016 – Samposium

Status Report: February 2016 – Samposium — Wed, 02 Mar 2016 01:48:11 +0000

[…] incorrectly arguing that ketchup should be applied to fries instead of mayonnaise and otherwise pretending to be Belgian. I took with me two different potential representations for the metahaplome and hoped to come back […]

Comment on Meet the Metahaplome by Status Report: February 2016 – Samposium

Status Report: February 2016 – Samposium — Wed, 02 Mar 2016 01:41:59 +0000

[…] At the end of January I gave a talk at the Aberystwyth Bioinformatics Workshop. The talk briskly sums up the work done so far over the first year-and-a-bit of my PhD and introduces the metahaplome: our very own new -ome, a graph-inspired representation of the variation in single nucleotide polymorphisms observed across aligned reads from a sequenced metagenome. The idea is to isolate and store information only the genomic positions that actually vary across sequenced reads and more importantly, keep track of the observed evidence for these variations to co-occur together. This evidence can be exploited to reconstruct sequences of variants that are likely to actually exist in nature, as opposed to the crude approximations provided by assembly-algorithm-de-jour. […]

Comment on Status Report: October 2015 by Status Report: February 2016 – Samposium

Status Report: February 2016 – Samposium — Wed, 02 Mar 2016 01:41:37 +0000

[…] facets of my PhD are currently in. Although I’ve briefly outlined the goal of my PhD in a previous status report, as of yet I’ve avoided exploring much of the detail here; partly as the work is […]

Comment on Fiddling with a Fitbit Charge HR by Meet the Metahaplome – Samposium

Meet the Metahaplome – Samposium — Tue, 01 Mar 2016 21:20:36 +0000

[…] a semi-interesting aside, I activated the workout mode on my Fitbit shortly before heading up to the podium to deliver my talk. My heart rate reached a peak of 162bpm […]

Comment on Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard) by How (not) to subset a BAM for GATK | Samposium

How (not) to subset a BAM for GATK | Samposium — Mon, 11 Jan 2016 22:09:05 +0000

[…] guess this is for the same reason that GATK requires a .dict and .fai file for references as I’ve discussed before, it just makes things a little easier for developers (and their code). In this case, the assumption […]

Comment on Duplicate definition error with GATK PrintReads and MalformedReadFilter by How (not) to subset a BAM for GATK | Samposium

How (not) to subset a BAM for GATK | Samposium — Sun, 10 Jan 2016 22:32:50 +0000

[…] to check whether these reads would fall foul of the infamous MalformedReadFilter with PrintReads (don’t forget, PrintReads automatically applies MalformedReadFilter) a completely different error […]

Comment on The Tolls of Bridge Building: Part IV, Mysterious Malformations by How (not) to subset a BAM with GATK and Picard | Samposium

How (not) to subset a BAM with GATK and Picard | Samposium — Sun, 10 Jan 2016 22:28:49 +0000

[…] wouldn’t be until later whilst investigating issues with another tool that I would discover how to correctly update the bit flags and read attributes to mark reads as unmapped as per the BAM specification. But in this instance, the error made me question whether I really […]