Here’s a wee puzzle: A mature Open Data focused journal (“Journal A”), owned and launched by an company or Institute (“Institute B”), developed into the flagship of an Academic Publisher (“Publisher C”), runs their own properly archived and citable blog with DOIs etc (“Blog D”). If a briefly published editorial Blog Post (“Editorial E”) disappears from their Blog, could it be an accident, or something else?
There were a few stickers on the lid, but why does my laptop look like this now? In short, I'm learning to touchtype a non-qwerty layout. My Japanese MacBook keyboard has 34 stickers for a custom layout I've been using a UK layout Microsoft Natural Ergonomic Keyboard 4000 for twenty years now. I wrote my PhD thesis on one (using the LaTeX typesetting language), and got a second matching one when I started working as a Post Doc.
I've recently been working what I considered to be a large scale FASTQ upload to the European Nucleotide Archive (ENA), from where it will be mirrored to the NCBS Short or Sequence Read Archive (SRA). Although the total size was "only" 37GB, this was about 3500 pairs of Illumina MiSeq FASTQ files - more than enough to make me worry about the job being interrupted and needing to resume without repeating uploads.
This is my first blog post in years - primarily down to a second child who is now a toddler. And what better topic to return to than a mainstay of past content, NCBI BLAST? This time with a motivating example from my recent work, metabarcoding. This is term used for sequencing a diagnostic region of DNA using specific primers for a group of organisms of interest, and then matching that amplicon to a database of known species.
All my recent blog posts have been looking at issues raised by the recent letter Shah et al. (2018) "Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows", and the associated test case which they ought to have included with the letter itself.
My November blog posts discussing the BLAST+ tools behaviour with an alignment limit setting (see What BLAST's max-target-sequences doesn't do, and the links from it), touched on database order, which comes into play as a tie breaker. Well, how is the BLAST database order defined?
This is the fourth in a series of blog posts seeking to throw light some of the claims about the BLAST+ tool recently published by Shah et al. (2018) "Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows". It was very frustrating that the letter did not provide a reproducible test case, but in reply to the first pair of posts (one and two, both on Friday 2 November 2018), lead
This is the third in a series of blog posts seeking to throw light some of the claims about the BLAST+ tool recently published by Shah et al. (2018) "Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows". It was very frustrating that the letter did not provide a reproducible test case, but in reply to the first pair of posts (one and two, both on Friday 2 November 2018), lead author Nidhi
This is the second in a series of blog posts seeking to throw light some of the claims about the BLAST+ tool recently published by Shah et al. (2018) "Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows". Since regrettably they did not provide a reproducible test case, my previous post began by introducing a minimal test case.
Back in 2015, my blog post "What BLAST's max-target-sequences doesn't do" highlighted what we called a scary BLAST+ -max_target_seqs bug, found and reported by Sujai Kumar. The NCBI BLAST teams took the stance this was a feature not a bug (and as a heuristic search tool, this is an understandable view), but conceded it could be better documented.
Another quick bug report blog post, this time NCBI Entrez's espell is currently broken returning: Couldn't resolve #PubmedSpellSrv, the address table is empty. Here's an example in full: $ curl -v https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?term=biopythooon *