Learning advanced analysis of gene regulation in Zaragoza

12. January, 2018

CSIC – Estación Experimental de Aula Dei (EEAD), Zaragoza, Spain

by Teshome Mulugeta, NMBU

I am so grateful to NORBIS that I was given the opportunity to travel to EEAD-CSIC, Zaragoza, Spain as a visiting PhD student. It was a useful experience to me to work and talk with several outstanding people. My visit to EEAD-CSIC was arranged and supervised by Dr. Bruno Contreras-Moreira. The primary goal of my visit was to spend time doing research related to my PhD with relevant professionals.

Research achievement

Upon arrival at EEAD-CSIC, I presented my PhD projects. We had a very productive discussion and I got useful feedback from relevant EEAD-CSIC research groups. We started by outlining the activities to perform during my stay at EEAD-CSIC. During my stay at EEAD-CSIC, I learned new proven approaches and methods to annotate transcription factors and their binding sites, to analyse expression based cis-regulatory motifs and to develop comparative database for orthology to be used for phylogenetic de novo regulatory motif discovery. The knowledge and experience i gained from EEAD-CSIC visit helped me to move my PhD projects forward.

Professional training

My presence at EEAD-CSIC provided me an opportunity to be invited to participate in one of the European Cooperation in Science and Technology (COST) action in Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) which was held in Lisbon, Portugal. The main goal of the workshop was to get a first hand hack-a-thon training from GREEKC resources and experts in gene regulation. The workshop helped me to assess the state of the art in gene regulatory process and its subsequent use in computational biology. I got the opportunity to discuss my PhD projects with trainers and trainee. I was active in the discussions and I believe my participation had a significant contribution in defining action points and future improvements at the end.

Professional network

My visit to EEAD-CSIC helped me to expand my professional network both in Spain and internationally especially at the GREEKC event that i participated in Lisbon. I met extraordinary professionals and experts in my PhD study area and had established a strong network with them. I am now active member of Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC http://greekc.org/) and will participate their annual workshops and trainings in the future.

Adventures and holidays

Zaragoza is located in northeastern Spain, Aragon region. I was fortunate to be in Zaragoza where the Pilar Festival (Las Fiestas del Pilar) is celebrated on the 12th of October. During the official celebration week, there comes wide variety of events like concerts, parades, flowers and theatre. It was amazing festival that brought people from every corner of Spain.

People show devotion to the Virgin del Pilar by leaving flowers

I had also the opportunity to revel in the incredible mountain scenery of the Pyrenees Spain arranged by EEAD-CSIC work colleagues. The experience was a truly engaging and  captivating which has left me awestruck.

Hiking to the Pyrenees

Conclusion

In general, my visit was a very fruitful and enriching experience. I am grateful to NORBIS for providing this opportunity. I would also like to thank Dr. Bruno for the hospitality and assistance during my stay in Spain. I also would like to thank my supervisors Prof. Dag Inge Våge, Associate Prof. Simen Rød Sandve, Dr. Torfinn Nome and Prof. Torgeir R. Hvidsten. Thanks for EEAD-CSIC colleagues and staff for their kindness and warm welcome.

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Want to organise a course or a workshop with support from NORBIS?

19. December, 2017

Do you carry an idea for a course or a workshop within the fields of bioinformatics, biostatistics or systems biology? Want to invite international experts to give lectures at this event? Once again it is time for NORBIS to ask you to propose a course or a workshop to be organised with financial and administrative support from us. We welcome brand new ideas, as well as adaptations of already existing courses and workshops.

Our financial support will cover travel related expenses for invited and internal lecturers as well as participating student members, for both courses and workshops. For courses, we will in addition give a flat sum of 60 000 NOK per course to the responsible department, to compensate time spent preparing and teaching the course. Our administrative support may help during both planning and execution of the course or the workshop, and will ease the process of making a course available across institutions.

Please visit this page to get an overview of the activities that we already offer, and to read our guidelines.

Our members currently have the following topics on their wish list (among many other!):

– basic and advanced statistics
– proteomics analysis (statistics and bioinformatics)
– machine learning
– high dimensional data analysis
– small RNA analysis
– network biology
– programming and reproducibility
– open source data

You are of course free to propose other topics within the scope of NORBIS.

We aim for our courses to be organized in a biannual fashion. We therefore encourage organisers of previous NORBIS courses to apply with an updated proposal, and to kindly add a summary of the participation and evaluation from the last round, as well as a note describing any updates and changes.

Please read more and register your proposal here: by  1^st March 2018.

The same principles behind the internet, social networks and biological networks

14. December, 2017

Illustration: Colourbox

NORBIS, supported by CCBIO, DLN and CBU, recently hosted a workshop on “Network Biology/Integromics Bioinformatics – Applications Towards Medicine” at Grand Hotel Terminus in Bergen, August 23rd-25th 2017.

Konstantina Dimitrakopoulou and Eli Synnøve Vidhammer at CCBIO have written a nice report about the workshop at the CCBIO webpages, which you can read here.

In association with this workshop, keynote speaker Professor Albert-László Barabási gave an exciting Horizon lecture at the UiB Faculty of Mathematics and Natural Sciences, this can now be enjoyed here.

More photos from the workshop are posted at our Fabebook page here.

Meeting Albert-László Barabasi after the lectures; including Inge Jonassen, Konstantina Dimitrakopoulou, Eileen Marie Hanna and Christine Stansberg.

A report from our third annual national conference at Sommarøy

14. December, 2017

Snorre Sulheim has written a nice report from our third conference at Sommarøy, for the Centre for Digital Life Norway here, thank you so much Snorre!

For more photos from the conference, please see our Facebook albums here and here.

An autumn with Bayesian approaches in Vienna

14. December, 2017

Hi, my name is Aliaksandr Hubin and I am a PhD student at the department of Mathematics of the University of Oslo. In this report I would like to share my international exchange experience, which took place in Autumn 2017 and was funded by the NORBIS travel grant.

During my exchange I was staying in Vienna, Austria for a period of 3 months (from September to November 2017). There I was visiting Dr. Florian Frommlet, an assistant professor in statistics at the Center for Medical Statistics, Informatics and Intelligent Systems of Medical University of  Vienna.

During the stay we have been working jointly on several projects. First of all we continued the collaboration and applied previously developed MJMCMC and GMJMCMC algorithms to GWAS studies. Performance of the algorithms was compared to other popular Bayesian approaches to GWAS such as MOSGWA and PiMass. The comparison was made on several simulation scenarios. Now the real data analysis is to be performed to finalize the paper. The results are to be published in the article entitled “A comprehensive study of Bayesian approaches to Genome-Wide Association Studies” written in collaboration with Michael Hagmann, Bernhard Bodenstorfer, Artur Gola, Małgorzata Bogdan, and Florian Frommlet.

Additionally we were finalizing the paper entitled “Deep nonlinear regression models in a Bayesian framework”, written together with Geir Storvik and Florian Frommlet. In this paper we have introduced the concept of a Deep Bayesian Regression model, which generalizes logic regressions, neural networks, fractional polynomials, and tree based regressions (and some other statistical learning approaches) into a flexible and general Bayesian framework. We then have suggested several algorithms for fitting DBR models. Several inference and prediction based examples were studied. In particular we have shown that the approach allows to recover highly nonlinear physical laws (like for example the 3rd Keppler’s law) in a closed form with a large power and low proportion of false positives. Additionally it showed good performance in asteroid and breast cancer classification problems. Finally some epigenetic study was performed with a goal to find optimal structure of dependence between the epigenetic observations and genetic factors in Arabidopsis thaliana.

Within the exchange duration I have given a talk entitled “Deep nonlinear regression models in a Bayesian framework” within Wiener Biometrische Sektion series of seminars. I have also had a chance to attend several other talks within Wiener Biometrische Sektion seminars and the as​ ​ autumn seminar “Young​ ​ Statisticians”, held at the Medical University of Vienna. Apart from that I attended the doctoral thesis defence of one of the fellow PhD students. This was an extremely interesting experience too, since the defense procedure was quite different from what I had seen in Norway.

The last but not least I met extremely interesting people carrying out advanced research in medical statistics ranging from clinical trials to survival analysis.

To conclude, I would like to thank NORBIS for an opportunity to spend these fantastic three months in beautiful Vienna, where not only I carried out some interesting research, but also had a chance to enjoy the imperial architecture and see numerous performances at the Opera House and Volksoper.

Learn ‘High Performance Computing in Bioinformatics’

5. December, 2017

Want to learn how to effectively use HPC clusters for running computationally or data intensive bioinformatics applications? Register now to join our course on ‘High Performance Computing in Bioinformatics‘, which runs in Oslo 16-27 April, by Torbjørn Rognes et al.

Read more and register here by 1st February (for obtaining credits, the deadlines are as follows; 11th January for UiO students, 3rd January for external students). Note the early registration deadline, which is due to UiO’s internal administrative deadlines for registering to courses

Register now for ‘Statistical methods in relatedness and pedigree analysis’

29. November, 2017

A report from the Center of Systems Biology in Reykjavik, Iceland

27. November, 2017

by Kjersti Rise, NTNU

I hadn’t really given a research stay abroad much thought when I started my PhD, it seemed like fun, but too much extra work in order to make it happen, and there were so many other things I already had to do. Then suddenly one day well into my second year everything changed, and I was writing applications and talking to scientists abroad, and about two months later I was on my way to the Center of Systems Biology in Reykjavik, Iceland!

Thanks to the travel grant from NORBIS, I ended up having the time of my life. I got to work in an exciting group, learning how to create and use genome scale models of cells, further develop code for these analyses, meet new people, and I got to discover Iceland! Working on a (for me) new topic was challenging, it required a lot of work, but I also learned way beyond what I had expected. It helped me learn a new programming language, a new way of thinking, getting a new perspective on possibilities in analysing biological data, and develop me as a scientist. Working together with brand new people with different backgrounds than myself was also very interesting, and I learned a lot from working with them. I made both new friends and new connections, and hopefully some of these new connections will become collaborators in the future.

Although the Icelandic climate is not all that different from the Norwegian one, and most of the people living in Iceland speak fairly understandable English, it was still a both strange and wonderful experience living in a foreign country for a while. Iceland is absolutely stunning, and learning Icelandic is really not for the faint at heart. I fell in love with the country, the science, the language, pretty much everything, and that’s all thanks to NORBIS who supported me financially, and made it possible. Travelling alone and figuring things out by yourself in a foreign country is always a good way of learning a lot about yourself, and the world around you. It changes perspective, not only in regards to science and work, but also in the way one sees the world. Yes, there was a bit of work required to make it happen (most of it when I came home, actually!), but not as much as I initially thought, and it was all so worth it. I’m so grateful I got to have this experience, and I can highly recommend some time abroad to anyone!

Kjersti Rise, September, 2017

Funding available for international exchange!

27. November, 2017

Once more, we encourage you as a NORBIS member to spend part of your PhD period (at least 3-6 months) at an institution abroad, to benefit from international expertise and to expand your international network. We have funding available for such an exchange, and we now invite you to apply for financial support for your stay. Read more and apply here by 1st March!

Registration now open for ‘Sequence comparison and database search’

23. November, 2017

NORBIS is happy to announce that registration now is open for our course ‘Sequence comparison and database search’ (NORBIS901), which will run in Bergen 29 January – 2 February.

This course provides insight into methods for aligning biological sequences. Its goal is to present an overview of the basic concepts of sequence alignments and some of their applications with a strong emphasis on homology based multiple sequence alignment modelling, one of the most widely used method in biology. The course is based on our previous course ‘An introduction to sequence comparison and database search‘, which was run in November 2015, but is more advanced and will also include RNA structure based alignments.

Read more and register here by 2nd January 2018

Feel free to share the invitation with anyone who might be interested.