Women in computing: learning the ropes in bioinformatics
Exploring the basics of bioinformatics at the Earlham Institute - the rewards and the lessons learned.
Alexandra Veress came to study at Earlham Institute for three months as part of the Korcsmáros Group, where she learned how to apply computational approaches to biology. Working with Tamás and his group, as many can attest, is a great experience - and Alexandra left for Hungary with the desire to learn even more about the world of bioinformatics.
Here she fills us in on her experience at EI, life in the UK (and better than expected weather), the kindness of postmen, the amazing social life on Norwich Research Park, and conquering (almost) the Earlham Institute table football league.
It is amazing. Since bioinformatics is interdisciplinary it is admirable how the informatics can associate with the biology. Tamas’ work and his ongoing projects are quite brilliant. He has a huge group with very clever and helpful members. I preferred the weekly meeting, when we discussed our problems and/or progress, also involving group members based in Hungary and Brazil.
I think I got the best out of my visit with the help of Márton Olbei (my co-supervisor). I joined his project, and as a part of it I was working on the “Comparative networkomics of Salmonella virulence genes”. As a result, we could identify some characteristic differences among the gastro- and extraintestinal pathovars, which may have a role in host adaptation. I am very glad because Tamas seemed very satisfied with our work.
I am a PhD student at the Eötvös Loránd University in Budapest, Hungary and a microbiologist research assistant at the Agricultural Biotechnology Institute in Godollo, also in Hungary. My PhD research topic is about the “Investigation of the relationship between mobile genetic elements and their host bacteria”.
Our group in Hungary started a collaboration with Tamas Korcsmaros in relation to my PhD project. After this collaborative project, I thought that I would like to learn more about bioinformatics, especially network analysis. Then I applied for an EMBO short-term grant which supported my visit and I could work 3 months in his group.
The main goal of this visit was to become a skilled user of Cytoscape, a community standard network analysis and visualisation tool, and learn about the methods of network analysis.
Thanks to Marton, I am sure that returning home I’ll be able to carry out the analysis for my project on my own. I also learnt about the very basics of the Linux system, bash shell.
However, there are still so many things left that I could learn from them.
Shortly, my answer is the desire to return for a longer period.
Beyond that I have learnt a lot - I would not have imagined that at the end of my visit we would be planning to publish a paper from this work in the next year. Moreover, as a (half) member of Tamas’s group, I will join the lab meetings from Godollo and continue the collaboration in the future.
Alexandra Varess, visiting PhD student to Earlham Institute
I could get insight into many projects of the different institutes. There are collaborations between the groups and there are so many seminars held by presenters from all around the world. The best thing was that as a microbiologist I could also participate in the meetings of Rob Kingsley’s group.
Rob and Tamas have been working together for years as a tight collaboration between the Earlham and the Quadram Institutes. They successfully combine the bioinformatics with the experimental research.
I was worried about the “English” weather, but I cannot complain. I expected worse, so it was a pleasant surprise. Norwich is very friendly; the whole city is like a calm village. My favourite part was the riverside, the ambiance of the Pulls Ferry, and I also preferred walking among the ancient buildings in the small, but busy, city centre.
I have lots of good memories, but what I will never forget is when a postman gave me a lift. I totally forgot about an important meeting! I was almost there, but I knew that I could not arrive in time. He was parking and I saw him walking towards his car, when I explained my situation. It was a coincidence but his next destination was the same as mine. When I asked how to thank him, his answer was: “what does life mean if we can’t even help each other when we can?”.
My general aspect is that English people are cheerful and very kind. I am sure that I will be back, at the worst just for a short visit to my new friends.
As I arrived in Norwich, I picked up a city map and in my spare time I chose what I was interested in and visited those places. I walked a lot in Norwich city centre; I liked the market, I saw the castle and I was amazed by the Norwich cathedral and so on. I spent a weekend with one of our collaborators, Dezso Modos (He is also working with Tamas and us, as well) in Cambridge.
He showed me the places of interest; between them I preferred the Queens' College and the King’s College Chapel. We also visited the very famous pub, The Eagle, which is a must for researchers.
I travelled to Belfast, where I visited an “old” friend, and we had a trip to the wonderful Giant’s Causeway. There were also some programs for the group. For example, we had a lunch altogether when all members of the group were in Norwich, where we celebrated the success of the group. There was a housewarming and a Halloween party too.
Lejla, Amanda, Alberto and I had a trip to Stonehenge-Bath-Bristol-Windsor. With Matthew and Elena we went to Horsey Bay, where we saw the seals with their ever-so-cute babies. The social life was amazing; I also enjoyed table football in the afternoons and at the [Norwich Research Park] recreation centre.
I will start to learn the Python programming language on my own and I will have a weekly visit to the Hungarian part of Tamas’ group (for help, and to participate in lab meetings in the future).
Absolutely. I am starting to apply additional grants. I would like to be back from next September.
Alexandra Varess, visiting PhD student to Earlham Institute