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

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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.”