And the award for the most-retweeted-tweet-of-a-photo-of-a-slide-from-a-presentation-of-mine goes to…

On November 20th, on the last day of my employment at UC Davis, I gave an exit seminar. Jenna Gallegos, a PhD student at UC Davis — who works on the awesome Intron-Mediated Enhancement (IME) project under the supervision of Alan Rose — posted several tweets from my talk including this photo of one of my slides:

This tweet continued to generate interest (retweets, likes, and mentions) for most of the 20th November and for many subsequent days afterwards. The latest retweet of this tweet was today: 16 days after the original tweet! I find this amazing especially as the original slide deals with the topic of genome assembly. At the time of writing the tweet has had 369 retweets and 277 likes

I'm pleased that people have found my jigsaw analogy useful. Some people commented that this isn't the best possible analogy and pointed out various ways that it could be more technically accurate (including suggestions of shredding copies of books and trying to piece together the original).

While I accept that this isn't the most scientific way of depicting the many problems and challenges of genome assembly, it is hopefully an accessible way of illustrating the problem. Nearly everyone has tried putting a jigsaw together, but not everyone has tried reconstituting a shredded book. My exit seminar was aimed at a very broad audience and so I pitched this slide accordingly.

People can follow Jenna on twitter (@FoodBeerScience) and should, at the very least, check out her awesome twitter bio. If you want to know more about her work, here is a recent review of IME that she wrote:

Finding bogus bioinformatics acronyms sometimes requires a laser-like focus

jabba logo.png

A new paper has been published in the journal BMC Research Notes:

This name is:

  1. Bogus — the word 'genome' doesn't contribute any letters to 'LASER' and two letters ('S' and 'R') are not derived from the initial letters of words.
  2. Duplicated — there are at least two other bioinformatics tools called LASER (see here and here).
  3. Undiscoverable — you really need to search Google for LASER genome assembly before you see this as a top result.
  4. Ambiguous — large is a very subjective term. The authors imply that LASER is suitable for human genomes. These are larger than some genomes but smaller than others.
  5. Inconsistent — the paper reveals that LASER is built on the code of QUAST (Quality Assessment Tool for Genome Assemblies). This means you end up with the somewhat bizarre documentation for how to run the program called LASER:

The example included with LASER installation can be run as:

./quast.py testdata/contigs1.fasta testdata/contigs2.fasta \ -R testdata/reference.fasta.gz -G testdata/genes.txt \ -O test_data/operons.txt

The output of LASER program can be viewed in file: ./quast_results/latest/report.txt

So to run LASER just type 'quast'!

Learn my Linux Bootcamp…all from within a web browser window

I awoke yesterday to see a lot of twitter notifications on my phone. Sometimes this happens when I've written a post on this blog, but I hadn't added anything for over a week. Turns out that the activity was triggered by this tweet by Richard Smith-Unna (@blahah404 on twitter):

As the screenshot below indicates, Richard has worked some amazing black magic to enable a single browser window to contain a fully interactive terminal as well as a file viewer/navigator; all alongside a (slightly modified) version of my original Linux bootcamp material.

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This new interactive command-line bootcamp is a wonderful resource and means that the only barrier to learning some simple, but powerful, Linux/Unix commands is the availability of a web browser.

Richard explains a little about how he put all of this together:

The Infrastructure, including adventure-time and docker-browser-server, was built by @maxogden and @mafintosh. The setup of this app was based on the get-dat adventure.