It was in November 2014 when I first wrote about Diego Gomez. Tomorrow will see a court, in Colombia, decide his fate. (Article in French) He is facing a fine of up to $327 000 and four to eight years in prison for the sharing a scientific article with a colleague. This is something that many scientists do and which is sometimes necessary for our work. This case highlights the need to move to a world where all scientific articles are open access, i.e. free to read. Continue reading
At the beginning of this month, I had the pleasure of attending the VBC PhD Symposium. The symposium is a two-day scientific conference organised by a committee of students from the VBC PhD Programme and, this year, led by Jillian Augustine. Just like last year, I acted as a volunteer to help with the set up and running of the event. Unfortunately, I wasn’t quite as helpful as I had hoped to be as it happened not only at a very busy time for me but when I was sick — and lost my voice for almost two weeks!
The focus this year was “Mind the App: Applications that Bridge Biology and Technology” and had talks that covered a variety of topics from using spider webs to study virus survival to brain-computer interfaces to the history of biological warfare. I do not mean to cover the entire symposium in detail and will merely focus on a couple of aspects which were of particular interest to me. Continue reading
I finally have the first publication from my PhD out! It’s quite a nice paper too which took a lot longer than expected. And it’s also open access so everyone can read it! If you do, you’ll learn about a new system we have set up for understanding plant pathogen interactions with the fungus Ustilago bromivora and the grass Brachypodium distachyon.
My contribution to this is almost entirely in bioinformatics. The genome assembly had been performed before I joined the group, but I did the genome analysis and comparative genomics, starting off visiting some collaborators in Munich. This was quite nice; going in a direction which is becoming more and more important and taking things further than I had before. Continue reading
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.
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
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!
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.
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.
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.”