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Dissertation for Xiaokang Zhang!

28. October, 2020

Friday 30th at 10:15, NORBIS PhD member Xiaokang Zhang is defending his PhD thesis entitled “Biomarker Discovery Using Statistical and Machine Learning Approaches on Gene Expression Data”.

NORBIS congratulates!

To follow his defense, see who have defended their thesis lately and who will be next, please see our Dissertation site.

6th NORBIS Annual Conference

28. October, 2020

The 6th NROBIS Annual Conference will due to the Covid-19 situation be different than normal years. This year we will organize the conference as a hybrid meeting over one and a half days. We plan for the meeting to be streamed online and the different partner institutions that can, arrange a local gathering for those who will/can meet in person.  This depends on local restrictions.

We also want to encourage supervisors and other researchers to join our meeting, both to facilitate discussion across several levels of experience, to inspire our students, and to increase your own national network.

We have student talks, poster sessions and keynote speakers. See program HERE.

Boston University research stay by Snorre Sulheim

22. October, 2020

Last winter I was able to spend 6 months at the Daniel Segrè lab  at Boston University thanks to financial support from NORBIS and SINTEF. I arrived on October 1st 2019, in time to enjoy the fall season with beautiful colors, nice weather and good opportunities to explore Boston.

Because I found it difficult to decide on a long-term housing option prior to my arrival I spent the first 10 days in an AirBnB that was a bit too far from the city center. Due to the extreme number of Universities in Boston housing is very expensive, and it was difficult to find something that was acceptable with respect to price and standard. After nearly being scammed twice in my effort to find an apartment on craigslist, I finally found a reasonable long-term flat through https://junehomes.com/  that I shared with 5 other. This worked surprisingly well.

Figure 1: Watching Boston Bruins beat Vancouver Canucks at TD garden.

Daniel Segrè hosts a moderately sized group (8 PhDs and 2 researchers) that works both experimental and computational aspects of microbes and microbial interactions. The quality of their work was impressive and it was very motivating to collaborate closely with these people. I learnt a lot of microbiology and ecology from the group meetings and journal clubs. Another cool aspect of working at Boston University is the proximity to other top-notch research institutions and therefore easy access a lot of relevant conferences, meetings or other research groups. To get the most out of my research stay I wanted engage in their ongoing projects and I ended up studying the fascinating phototrophic marine bacteria Prochlorococcus (preprint on BioRxiv) using an updated genome-scale metabolic model. To understand how the metabolism of Prochlorococcus is affected by nutrient limitations and diel cycles we simulated growth using COMETS. To facilitate these simulations we developed light absorption and time-dependent light availability as new features in COMETS (read about the recent COMETS release on arXiv).

My research stay ended abruptly with the arrival of covid-19, but I was satisfied with my stay. I can highly recommend a research exchange to Boston. I addition to great science, Boston also offers an active running community and reasonable access to (disappointing) skiing in winter. The public transport is average, the traffic is one of the worst in US, but the city is small enough that you can easily bike anywhere. By a refurbished race bike at https://bikesnotbombs.org/ if you want to get the most out of your stay.

Figure 2: There is also good skiing in North America, but not close to Boston.

New director of NORBIS

16. October, 2020

NORBIS has gotten a new director!

 

 

On October 1st, professor Susanna Röblitz took over the position as director of NORBIS. Susanna is a group leader at Computational Biology Unit (CBU) at University of Bergen (UiB). Her research group focuses on the construction, simulation, analysis and optimization of dynamic, mathematical models for biological and biochemical processes on different levels of organization. You can read more about Susanna and her research at CBU and UiB.

 

We would like to thank our former NORBIS director, professor Inge Jonassen, and we are happy that he will continue to be a part of the NORBIS family as a member of our scientific advisory board (SAB).

NORBIS Covid_19 webinar mini-series

22. May, 2020

To present some of the work done related to the novel disease Covid_19, NORBIS is arranging a webinar mini-series.

First lecture is May 27th at 12.30. The lecturer is Kyrre Lekve from Simula Research Laboratories and topic is “Smittestopp”. Kyrre Lekve is Deputy Managing Director at Simula Research Laboratories and also member of the NORBIS scientific advisory board.

Second lecture will be June 17th at 11:00 by Inge Jonassen, professor at CBU/UiB and director at NORBIS and head of ELIXIR Norway. Topic for this lecture is “ELIXIR – sharing of biological data – and efforts linked with the Covid-19 pandemic”.

 

Registration for the webinar miniseries can be found HERE.

International exchange report from Xiaokang Zhang

6. April, 2020

With the support of NORBIS, I visited Professor Bernhard Palsson’s group, Systems Biology Research Group, in University of California, San Diego, USA, from September 2019 to February 2020.

 

The original plan was actually from May to November 2020, but my application of the US visa was pending in the so-called “administrative process” for four months. But this delay took me to UCSD right at the beginning of the new semester. There are good and bad of that: good thing is that there were lots of welcoming activities on campus; bad thing is that accommodation is in short, especially the flights and (temporary) accommodation were almost booked at the last minute because I couldn’t make any travelling plan before I got the Visa, and the long-term accommodation was booked after I arrived there when most of the resources had already been reserved by the freshmen. So advice from me will be: plan ahead and start the paperwork early.

 

Bear at Jacobs School of Engineering, UCSD. Photo: Xiaokang Zhang

 

The campus of UCSD is in La Jolla, 20 minutes’ drive to the north of San Diego downtown. Everything in La Jolla is far away from each other. Even though it’s a good opportunity for walking since it’s very sunny almost the whole time (and for Bergen, it’s rainy or cloudy almost the whole time 😉 but walking from my apartment to the campus is 40 minutes, and another 40 minutes to the nearest supermarket. Public transportation is sort of useless. But that’s a common problem for the people who don’t have a car, so carpooling is very popular. So that problem can be naturally solved after you make enough friends.

 

My main job there is to continue our collaboration which already started one year before I went there. Carrying particular questions in mind, my work started immediately after I arrived. The first problem solved was visualization of our draft reconstruction model. With the help of Zachary A. King, the main developer of Escher (https://escher.github.io/#/), and the others in the Escher group, our ugly and messy metabolic map was replaced with an elegant and informative Escher map. From there, I worked closely with Daniel Zielinski to explore the draft model. Our work was later presented in the conference Winter Q-Bio 2020 (https://w-qbio.org/), and will also be included in the manuscript currently in preparation from dCod project (https://www.uib.no/en/dcod).

 

Besides the project mentioned above, a paper from our previous work (An Ensemble Feature Selection Framework Integrating Stability, DOI: https://doi.org/10.1109/BIBM47256.2019.8983310) was accepted as conference proceedings paper in BIBM 2019 which happened to take place in San Diego two months after I went there. Another manuscript was also finished and submitted to BMC Bioinformatics during my stay there, and it was accepted just before I came back to Bergen (RASflow: an RNA-Seq analysis workflow with Snakemake, DOI: https://doi.org/10.1186/s12859-020-3433-x).

 

NCAA football match UCLA vs. CAL. Photo: Xiaokang Zhang

 

By attending the group meeting every two weeks and the group’s winter retreat day, I got to learn the many interesting research topics going on in the group and was also shocked by the large publication number shown in the annual summary on the group retreat day.

 

Overall, it was an excellent research visit with lots of research input and output, and also lots of cool friends, good food, beautiful beaches, sunshine.

 

Laguna Beach. Photo Xiaokang Zhang

Register now for the “High Performance Computing in Bioinformatics” course

8. January, 2020

Registration is now open for the NORBIS course “High Performance Computing in Bioinformatics”, which will take place at UiO, Oslo, March 23rd – April 3rd, 2020. This course will focus on the application of high performance computing (HPC) to bioinformatics analysis, and is organized by Torbjørn Rognes.
 
You will find more details about the course and how to register hereRegistration ends February 21st, and successful applicants will be notified shortly after this date.

Report from the 5th Annual Conference of NORBIS

15. October, 2019

Entrance to the fortress

 

The 5th Annual NORBIS Meeting began with a ferry ride across the fjord to Oscarsborg fortress. The boat looked extremely serious as it approached us with the island and fort in the background, reminding us of the history of Oscarsborg! We then were off to a strong start, with Sushma Grellscheid giving us an excellent, memorable talk on cytoplasmic phase separation, before dinner and the first evening poster session.

 

Left: Sushma Grellscheid, right: poster session

 

The next morning, Kjetill Sigurd Jakobsen started our day discussing the Earth Biogenome Project before we had our first round of student talks, where we were lucky enough to get a private showing of two Forsker Grand Prix talks from our very own NORBIS contestants; Joseph Diab and Christian Schulz. After the PhD student forum and discussions across lunch, we headed to the lawn in the centre of the fortress to compete against each other in various challenges, where our problem solving and teamwork skills were put to the test!

 

Winners of the team-building contest

 

To make up for the afternoon spent in the sun, we had another round of student talks and the final poster session before closing the scientific aspect of the day. At dinner that evening, there were smiles all around as the winners from the afternoon activities and the student poster sessions were announced and the room was introduced to our new student representatives. The food and the discussions were excellent, and many of us found ourselves continuing the evening at the bar.

The final morning concluded our conference extremely well, with Jukka Corander giving an engaging talk on bacterial pathogen evolution before our final round of student talks. Our own Ines Heiland then gave the closing talk of the conference, allowing us to finish on an outstanding note. After a final hearty lunch, we took the ferry back across the fjord and said our goodbyes as the coach took us back into civilization (Oslo).

 

Written by Chloe Rixon (IEMR, UiO)

All photos by Kari M. Ersland

Report from the NORBIS summer school 2019

21. August, 2019

A great week at the University of Tromsø!
 
We started the week with an in-depth perspective into the importance of metabolomics, courtesy of our guest lecturer Hans Stenlund from the Swedish Metabolomic Centre, university of Umeå. He ensured we gained a detailed understanding of how we can attempt to study and capture the metabolome, and most importantly, analyse the resulting data!
 
Our evenings allowed us to regain some energy spent understanding these complicated concepts, first of all with an invigorating hike (or cable car ride) up Fløya mountain, and secondly, with a very competitive (and fun) round of mini-golf and beers and Storgata Camping.
 
On top of Fløya mountain. Photo: Joseph Diab
 
The third day was spent recuperating from both the drinks and the metabolomics, as we delved into proteomics; translating some of the concepts into reality with a fascinating visit to the proteomics lab at UiT’s IFA.
 
   
Photo: Joseph Diab
 
Thursday was the last day of lectures, where Ines and Joseph tied the week together by covering systems biology and pathway modelling/analysis as a whole, and we spent our last evening together having pizza and drinks, migrating from Pepe’s pizza to Tromsø’s historical Ølhallen.
 
Ines Heiland giving a presentation. Pizza in the sun! Photo: Joseph Diab
 
On the last day, Friday, I think we all had a lot of new information to take in and were feeling inspired to apply the theory that we had learnt during the week. This was especially clear when listening to the presentations which some brave attendees had volunteered to give, showing us what they had put together in the practical sessions during the week.
 
All in all, the summer school had a very enjoyable, informal and friendly atmosphere, mixed with informative lectures on very useful topics, making for a great week in a beautiful location! Thank you NORBIS, Hans, Ines and most of all Joseph for organizing the week!

Register now for the “Metabolic pathway analysis” course

9. August, 2019

Registration is now open for the NORBIS course “Metabolic pathway analysis”, which will take place at NTNU, Trondheim, 4-8 November 2019. This course will provide an introduction to computational analysis and reconstruction of both small and genome-scale metabolic networks, and is organised by Ines Heiland.
 
You will find more details about the course and how to register hereRegistration ends September 15, and successful applicants will be notified shortly after this date. Note that external students must register here before September 15 to get credits for this course.
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