2017-01-27

Mozilla Science Fellowship application 2016

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 is due to the timing of personal circumstances - I'm now a father, and despite the taking time off under the UK's Shared Parental Leave scheme, I'm currently trying to cut back work related activities.

While preparing my application, I was impressed by Jon Tennant's decision to post his application openly online, and had been meaning to share mine too. Better late than never?

[Update: To be clear, this was my application in 2016, which was shortlisted but ultimately unsuccessful]

[Update: Cross-posted on the James Hutton ICS blog]

2017-01-25

Achievement Unlocked: Shared Parental Leave

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.

The UK's new SPL system was introduced in April 2015, and is intended to allow working couples to share a year off after the birth of a child. The basics of the UK SPL scheme and Statutory Shared Parental Pay (ShPP) rules are laid down in law, but good employers will pay the father more than the statutory minimum.

2016-05-13

Automatically keeping a GitHub fork up to date

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.

How can we automatically mirror the upstream repository? Enter GitHub Deploy Keys, which we can use to grant read/write access on a repository basis - which a cron job can use to push changes to our mirrored git repository.

2015-12-18

What BLAST's max-target-sequences doesn't do


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.

2015-07-08

BLAST XML 2 - does the sequel live up to my hopes?

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. Sadly the worries voiced on the OBF Bio* mailing lists were well founded.

In part because XML is so verbose, it is nice to be able to parse it as a stream - meaning capturing the output via stdout and Unix pipes. That appears to be "broken". In fact, producing a bundle of XML files using XInclude seems a recipe for trouble.