Wednesday, 30 November 2016

2016 - what a year that was (for Genome-scale bioinformatics!)

MIBTP Master Class: Day 1 

Thursday 1st December 2016

Right so here we are again, writing an example post for the MIBTP Master Class on "Genome Scale Bioinformatics with Galaxy" in 2016. Its been a rather "eventful" year all in all and I am really hoping that this Master Class will be distinguished by being mostly "uneventful"!

So despite making all the plans and preparations that seem reasonable we are once more embarking on that most tricky of teaching adventures: a workshop using a live, public resource upon which the whole learning opportunity hinges. As ever we can put in place contingencies and hope for the best, but the worst case scenarion is always the one in which we only learn one lesson - don't rely on public web servers!

Anyway the material is deployed, Galaxy is up and we have a bunch of keen students so... (as my favourite Doctor would say) Allons-y!

Thursday, 13 December 2012

MIBTP: Masterclass on Galaxy Day Two...

MIBTP: Masterclass on Galaxy Day Two...

Today is the second day of the MIBTP Masterclass on Genome Scale Bioinformatics with Galaxy... (gosh I wish I could type!)

OK - a very frosty morning meant I was nearly late as the handbrake of the car was frozen on - abandoned car, got on bike... went back to car and chocked fron wheels -parked on a hill, visions of unfreezing handbrake propelling car into busy junction.... back on bike!

Enough about me...

Students trying (and so far suceeding) to get the whole genome analysis of Archbishop Desmond Tutu's exonic SNPs running on Galaxy - start off with importing the SNPs from 5 entire personal genomes into a Galaxy history (~11 million line file - take that MSExcel!)...

Then to filter on Ns and places where ABT does not differ from the reference genome... This involves altering the filter command to exclude the requirement to only select Chr22 SNPs - we want to do the whole genome! (also a somewhat existential discussion on the meaning of N...)

Still it's dark in Pennsylvania....

Wednesday, 12 December 2012

MIBTP: Galaxy - First Day roundup...

MIBTP: Galaxy - First Day roundup...

Okay so we survived the first day of the MIBTP Galaxy workshop, getting a small group of First Year PhD students from Warwick, Leicester and Birmingham to do some analysis exercises on the Galaxy public server.

Galaxy was largely snappy and well behaved, despite using (mostly) Win7 and IE machines. One issue that did arise was the visualisation of SNPs on exons in the "Finding the Exons with the most SNPs". Looked great in the screencast, but page neverloaded and IE gave a "script taking too long to respond error". This suggests that the issue is a javascript problem, but will have to investigate.

Also links out to display using genetrack did not load, but ensembl did.

Really hoping that the workflow viewer is not affected (that's tomorrow's problem!).

Still, basically things worked as planned, but timing was rather off! 

Okay, here we go!

Okay here we go....

So we are starting the first practical session of the MIBTP Galaxy workshop here in Leicester...

SOO far Galaxy is behaving itself and apart from a few problems getting everybody online (eduroam is not the universal panacea to all network issues!) everybody is working through the first Galaxy Screen Cast:

  • Hopefully this will prove straightforward and we can get onto the group tasks...

    Monday, 10 December 2012

    Day One: Blogging the Galaxy...

    Day One: Blogging the exploration of Galaxy on the MIBTP2012
    This blog post is the first of a series of test posts using the Blogger platform for making notes on bioinformatics analysis using the Galaxy online resource.
    Using a blog means that notes are stored securely online, they can be accompanied by rich content (links, images etc) and accessed where ever you are!

    Getting started
    So lets assume that you have gone to the Galaxy website, setup an account and are all logged in, and this is what you can see:

    Nice windows, with lots of history!