Thursday, December 31, 2015

Closing the books on 2015

The last line of Perl has been written, the last SQL select executed. As 2015 draws to a close, I want to extend a thank you to everyone who has read this blog, commented on it here or over on Twitter, followed me on Twitter, engaged me on Twitter, or any of the other myriad of ways that suggest that what I write and tweet is of interest to others. It is very rewarding to know that others find this space engaging, and I hope to continue to earn your attention and time.

So long 2015.  I mustered a bit more resolve this year than previous years, hitting the 5th most number of posts for a full year (which should make it the median). 2016 promises to be an exciting year in the sequencing and genomics arena and I will try to both up the frequency and reduce the variance in the frequency of these posts -- ideally while improving the quality.  Will I succeed -- only you, the reader, can score the quality aspect.

Loose 2015 Threads #2: Thanks for the help with bootstrap values

I owe a belated thank you to everyone who responded to my post on my muddled thinking around phylogenetic tree bootstrap values.  I think I'm straightened out now and even dare to think I can explain this to someone else. 

Wednesday, December 30, 2015

Loose 2015 threads #1: MiSeq 2x300 Issues

Before 2015 ends, I'd like to tie up two loose threads.  In doing so, I'll deviate slightly from my usual pattern and publish two posts in a day; I could have lumped them together but instead I'll split.  First up, a belated explanation, prompted by a comment, of my mention of issues with the MiSeq 2x300 reagents and a bit more on my confusion with regard to bootstrap values.

Monday, December 28, 2015

Thoughts on the Synthetic Biology of Seveneves

Neal Stephenson's Seveneves is a sprawling space novel of truly epic ambition and scope, which I enjoyed thoroughly.  I'm not going to review it or give a detailed plot summary, but there are aspects related to the biology angles which interest me enough to scribble -- which means I must reveal some key plot points.  I've grown increasingly sensitive to spoilers and (yo Charles Schulz's ghost: thanks for wrecking Citizen Kane for me at a young age!) for myself prefer to go into a major book or movie as cold as possible.  So, if you haven't read the book and were planning to do so, please don't jump beyond the jump break.  If you do, don't blame me for any reveals!

Friday, December 11, 2015

MinION and Time-to-Result

Peripatetic blogger Dale Yuzuki posed a question on my last piece which I'll answer with a separate post because it crystallizes for me what makes the Oxford Nanopore platform so different for a large number of counting-type assays.  Dale's question was on Zev William's talk on pre-implantation screening and the number of reads required.

Monday, December 07, 2015

MinION Community Meeting 2015: Reflections & Wrap-Up

I spent the end of last week at the New York Genome Center for Oxford Nanopore's MinION Community Meeting 2015.  Since the family joined me for the weekend, I let my thoughts simmer for a wrap-up.  Plus I've been spending time scrutinizing the complementary "pen" for a USB connection and sample port, with no luck.  Wisely, I've given up on that -- so I can start the same process with the "notepad".  I've also finally stopped looking over my shoulder for a pitchfork-and-torch crowd after my numerous Twitter miscues, ranging from omitting speakers' names and affiliations to various mutations of the official hashtag (when I remembered any hashtag).  For a slightly better synthesis of the Twitter stream, see my Storify.