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 *

I've not managed to blog much at all this year (parenthood), so here's a quick BLAST+ bug report from working on updating the Galaxy wrappers: I've found a reproducible segmentation fault in tblastn under both Mac and Linux when requesting HTML output. Sample FASTA data files four_human_proteins.fasta and rhodopsin_nucs.fasta are examples I use often as test cases.

Last summer I applied to the  Mozilla Fellows for Science 2016 call. Congratulations to the four 2016 fellows, selected from an impressive 483 submissions for only the second year of this innovative program. I was delighted to be short listed and interviewed, but also slightly relieved not to have made the final cut.

This year was a first for my employer, the James Hutton Institute, and potentially all the UK research institutes on BBSRC employment Terms and Conditions: A father has taken time off work using Shared Parental Leave (SPL). That's something to be pleased about, although to me overshadowed of course by becoming a father.

We recently setup a departmental GitHub account for Hutton ICS, and one of the things we'll use this for is to showcase projects which ICS staff are contributing to - such as Biopython in my case. To start with we have forked https://github.com/biopython/biopython as https://github.com/huttonics/biopython which we'll use as a read-only mirror - but now we want to keep it up to date with commits pushed to the upstream repository.

This is a short post to highlight a scary BLAST+ -max_target_seqs bug found and reported by Sujai Kumar, which he discovered in the course of working on some puzzling Blobtools output while analysing the tardigrade genome.

Last year I wrote a blog post "BLAST XML output needs more love from NCBI", and in the numerous updates to this, tracked the NCBI outreach and then release of BLAST XML 2. The new output format was included in BLAST+ 2.2.31 as output format 15, without any kind of beta release for user feedback. Later than planned, I was able to give this a try during the Galaxy Community Conference 2015 Hackathon.

Recently NCBI BLAST+ 2.2.31 was released, and it contains an undocumented "Easter Egg" - this is still very rough around the edges but they're working on SAM format output!

Here's a little back-story on my latest preprint (based on my email to samtools-devel), which went live on the biology preprint server bioRvix at the end of last week: The current version is a terse three pages (trying to meet an "application note" page limit), but nevertheless should clarify the intended usage of these parts of the SAM/BAM specification.

This is another brief NCBI BLAST+ bug report blog post, about a regression in BLAST+ 2.2.29 which will be breaking existing pipelines around the world. The problem is a new " feature " which treats an empty query file as an error.

Dear Santa, Please could you ask the Elves at the NCBI to deliver the following BLAST+ feature requests for Christmas 2014? Thank you, Peter P.S. Do they think I have been naughty or nice with my BLAST blog posts? These are roughly in order of increasing priority, starting with some relatively minor issues.