VBC PhD Retreat 2016 Report

This was something I wrote about two months ago. It was meant to be published on the VBC website but it’s been delayed so much I figured I might as well just put it out here. It seems a waste to just forget about it otherwise. I would’ve included some pictures but I’m not sure where my pictures are. When it gets posted on the VBC website there should be some pictures from other people.


Aim

A few weeks ago, the merry students of the VBC set off for the 2016 PhD Retreat – two days of science, fun and camaraderie – that was organised by the PhD representatives. This year was my second retreat and the location was the Schloss Hotel Krumbach , just a short distance outside of Vienna. Subsequently, Ines asked me if I would be willing to write a short report on the retreat and what follows are my thoughts. As I was not taking detailed notes, rather than just a run-down of what happened I have chosen to take some main events and expand upon them and how I feel they fit in a larger context. Continue reading

Long Night Of Research

About two weeks ago I was involved in a public outreach programme, the Lange Nacht der Forschung (Long Night of Research). This was a series of events around Austria that had scientific organisations sharing their research with the public. I was one of the volunteers at the Gregor Mendel Institute‘s display at the Heldenplatz in Vienna. According to the head of public relations from the Austrian Academy of Science, about 12 000 people passed through the display tent!

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Part of the GMI display with me in the background. (Source: APA)

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Inside Out: Oscar for originality?

Sometimes the smallest niggles can bug one the most. So it was when I saw an article on Slate that wanted to award Inside Out the discontinued Oscar for Best Original Story.

The Best Original Story Oscar existed between 1928 and 1956 to honor the writers who came up with the idea or treatment for a film but may or may not have actually written the script. This year’s award goes to Pete Docter and Ronnie Del Carmen for Inside Out, which featured one of the most original narratives in recent memory.

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On hiatus

By this point, it’s probably fairly obvious that this blog is on hiatus. I’m afraid I just don’t have the time to create new posts at the moment. It’s not a shortage of ideas – as I have had several, some which would’ve been really cool to put together – but just a question of what I can manage at the moment. I don’t want to just leave it hanging empty, so, this post will serve as a thank you to everyone that has read my blog and a promise to bring back to life when I have the time available.

My Viennese library

It’s not nearly as impressive as what I had back in Cape Town (Books were too big and heavy to take with me.) but it’s slowly growing.

My Viennese library

My Viennese library

I got I Wish I’d Made You Angry Earlier for free! During the introductory talk by the campus librarian, he gave us a short challenge to complete and the person that found the answer first would get a book. (In the end I believe he actually gave away two books because the replies were so close together.) It was just a simple task to look up the number that specified where the book could be found in the library. The library, and a nearby research lab, is named after Max Perutz, who was born in Austria, making the book a suitable prize.

I only got Faith Vs Fact a few days ago but I’m quite excited. It was actually almost 3 weeks later than Amazon originally promised but I’ll try to forgive them for that. It’s Jerry Coyne’s latest book after Why Evolution Is True. It, obviously, deals with the methodological incompatibility of science and religion. Someone can be both religious and a scientist but that doesn’t mean the ideas are compatible. There are also, for example, judges that take bribes; but that doesn’t mean that that’s compatible with being a judge. Since I’ve been reading his blog (He insists it’s not a blog.) for years and other pieces on the topic, I doubt there will be much new. Still, it should be interesting and it’s nice to have everything succinctly put together.

Schönbrunn Tiergarten

A few weeks ago, some members of my lab planned a trip to the Schönbrunn Tiergarten (Schönbrunn Zoo) in Vienna, the oldest zoo in the world, and I went with them. In this post I’ll just share some of the better photos from the day. I should also note that I have not forgotten that zoos are seldom ideal. I take some solace in that, according to Wikipedia:

Today, Tiergarten Schönbrunn is considered and regards itself as a scientifically administered zoo which sees its main purpose as a centre for species conservation and general nature conservation as well as in the fulfillment of the education mandate given to it by the legislation.

Regarding that, I did, from time to time, keep an eye out for environmental enrichments. Obviously a brief visit is not going to give a great overview but I did see enrichment in some enclosures, so I assume that such considerations are taken into account. Continue reading

Some programming to share

I haven’t posted here much as my supervisor is a bit of a workaholic and its been tough to find time to do everything that needs to be done and engaging in healthy non-work activities. However, I have permission from my supervisor to share something from my work, a set of three simple scripts I wrote. All these scripts run in the UNIX shell.

They’re probably not the most efficient way to do things but, considering I only started to learn any programming last year, I’m rather proud of them. (I’m not counting some basic HTML or fiddling around with the OHRRPGCE plotscripting language which I used to do a few years ago.) You can find them here on Github.

For these to work I already had the correctly formatted protein sequences and gene groupings. The first script “aligningproteinfamilies” went through the list of groups and used T-Coffee to align those proteins. That result came out in Clustal format which I found tricky to work with, so I wrote “reformatclustal” to pull out only the bits that were important to me; the actual sequence and the consensus scoring. In the new format it was easier to look for a perfect alignment, find the position in the line and then extract the amino acid sequence corresponding to that position with “maxconslenresultv2.”