The ISBGroup Blog

This year will be an important year for our group, when many things will mature in various ways.

This will be the year when we will have to transform some of the student affiliations into scholarship students, and some of the scholarship students into Ph.D. student affiliations, and in this make use of our various sources of internal and external funding, and make use of all our collaborations with other groups. An example of the latter is our important collaboration with Freiburg, where I (Gunnar) have an external fellowship, and where half of Rikard’s employement is financed.

This will also be a year when we will will transform many of our almost finished projects into publications. Last year we grew substantially in personell, and this has allowed us a quite new work capacity, which we must learn to make use of properly, and make visible in terms of an increased rate of publications. Several papers have also been submitted or re-submitted in the last weeks, and with some luck, this will soon start showing off as new interesting publications, showing some of our ongoing projects more visibly to the rest of the world.

In this early phase of the year, we are also running the second edition of TSRT17, which is our own systems biology course. It is our intention that this year’s edition will be a clear improvement compared to last year, and that we just like last year will be able to recruit some of the most talented students as scholarship or project students.

One example of how this process is continuing is Mikael Forsgren, who took the course last year, has been employed in the group of Peter Lundberg ever since, and is now doing a little project also in our group, where he helps us finalize an interesting project on core-box modeling and back-translation. Two other new people in the group are Lovisa Österlund who is doing a boolean approach to the study of mTOR and autophagy and their relation to insulin signaling, and Gustaf Ullman, who will become our new expert on stochastic and single-molecule modelling and simulations.

We have also continued our team building activities, through regular whole-day meetings where we present our work for each other (see up-coming and previous events), through the continued application of wave and other online communication tools, and through various joint social activities such as weekly game-nights, and a joint vacation weekend in Romme. We also plan to expand our weekly meetings to include seminar-series with internal and external lecturers; this will also be a part of the continued launching and starting up of the Linköping centre for systems biology, which hopefully will also be stimulated by our upcoming recruitment of two world-leading systems biology guest professors.

All in all, we are moving into a very exciting year, where many of the plans and projects that were started last year hopefully will mature and bear lots of scientific fruits.

Summing up 2009, it must be said that it without a doubt has been the most important and expansive year so far, at least with respect to the systems biology part of the group.

Going into the year, there were only me (Gunnar), Cecilia “Ia” Brännmark, and two new students: Elin Nyman and Rikard Johansson. Then interesting and ambitious students appeared one-by-one, e.g., Robert Palmér, Fredrik Bäcklund during the spring/summer, Eva-Maria Hansson and Oscar Samuelsson during the early autumn, and Amanda Jonsson during the late autumn. This means that the group has more than doubled in size in a short period of time, and we have been in a very nice feeling of growth and “anything is possible” during the entire year. During this time we have spent quite some time to get a nice group feeling, creating our own home page, logga, name, and has also started to improve our internal communications through the adoption of the new and powerful google wave online communication tool. We had also to establish new routines for our internal meetings: we initiated weekly Monday meetings, and changed our joint supervision time where all students were present to entire supervision-days, all because of the rapid growth of the group.

2009 was also the year when TSRT17, our own course was launched. This is a project course that is held for 3rd years students at the Technical Biology program, and it will be held anually from now on. The project was done as a collaboration with the system identification/control engineering group at ISY (led by Torkel Glad and Lennart Ljung), and the MR-group led by Peter Lundberg. This course will be important for us to train and inspire students to be future project, MSc, and Ph.D. students in our group.

Another important event this year was to start the process of forming a systems biology center at Linköping University. We had a first meeting with all 15 groups, and have also combined these networking efforts with the participation in the formation of a national Wallenberg Institute for Systems Biology, and in various European network formations on systems biology of diabetes, several of which have been coordinated by us.

This important year will probably in many ways be remembered as the defining year of our group, and it is with great enthusiasm and anticipation that we move into the new year and into the new decade.

These last few weeks, I (Gunnar) have been almost completely buried under some high-maintainance application writing. Last week there was the deadline for submitting to CENIIT. This was stimulating as it marked the expansion of our group to the technical faculty, which is where I come from scientifically, and where I want to have and am establishing a strong second foot; in particular regarding methods for system identification.

Today, however, there was an even bigger deadline: to the FP7. It was a major network application, involving some 20 partners, 5 pharmaceutical companies, 12 MEuro, etc etc. It turned out very nice in the end, but keeping in contact with that many people is quite exhausting. Scientifically it was based on a continuation of Elin’s pilot study, extending the Dalla Man model to a multi-scale model also incorporating biochemical details.

Otherwise on the news front, Siri Fagerholm defended her mid-Ph.D. report last week (October 21).

When looking forward it is time to fix with the final arrangements so that we can launch the seminar-series associated with the Linköping Centre for Systems Biology, which should start in some 3 weeks or so. It is also time to start preparing in detail for next years edition of the Project course in Systems Biology….!

And it will be reaally nice to at last have time to do some science and supervision again! 🙂

Gunnar

Time is passing by, and several talks are on their way. Actually, today the first of them happened, via Anita Öst’s Ph.D. thesis defence. She defended her thesis “Lipid metabolism and insulin Signalling in Adipocytes – enhanced autophagy in type 2 diabetes”, with Anna Krok from Karolinska Institutet as opponent.

Next week, Gunnar Cedersund will present our work in general, and the ideas concerning unique estimation in unidentifiable models in particular, at ISY’s seminar-series on diagnosis. The details for this is as follows:
When: October 13, 10.15-12
Where: Systemet, ISY, Linköping University, Sweden
What: Unique identification in unidentifiable models, its development for systems biology, and its possible applications to diagnosis
For whom: All that are interested, it is centered around discussions, and very informal

Also on Friday in the next week, October 16, Gunnar will give a presentation of our work, again with a focus on the theoretical methods, at a conference in Hamburg. A link to this conference is found here. We recently found out that Hamburg has already established links with Linköping, in terms of possible exchanges between students, so it will be exciting to see if we can conribute to making good use of these possibilities.

Are you interested in Systems Biology? Are you located in Linköping/Norrköping, Sweden? Then, don’t miss this SystemsBiology@LiU-day, with 15 groups from 10 institutions! The day comprises lectures with overviews of the various groups, poster sessions, a Master Thesis Corner, an open discussion, and a more formal decision-making discussion. Hopefully, this day will lead to the creation of a LiU-wide network on systems biology, to a regular seminar-series/Ph.D. course with external and internal lecturers, and to the planning for a first edition of Linköping Conference of Systems Biology, in early autumn 2010.

More information can be found here.

This is the first entry in our new home page experiment: a group blog!

Right now, there are many things going on, and here is a short summary of some of the most exciting things.

– At Linköping university we are arranging an all day symposium on systems biology on Wednesday Sept 30. It is for and with all scientists working with systems biology at the university, and at the least 15 groups at ~10 different institutions are represented. I think that it is really cool that so many groups are already working with systems biology, and we hope that the day will be a success, leading to for instance the formation of University-wide network, a regular and joint seminar-series/Ph.D. course with internal and external lecturers, and the arrangement of a first edition of Linköping Conference of Systems Biology. More info here.

– Last week I was in Warwick, UK, and gave a lecture

Sound identification and model merging when studying type 2 diabetes on our projects at the MOAN break-out session at the International Conference for Complex Systems. Here is more information.

– A few weeks ago four of us (I, Cecilia Brännmark, Rikard Johansson, and Elin Nyman) went to the International Conference of Systems Biology at Stanford, USA. It was a very inspiring time, and we were happy to note that our group had the biggest Scandinavian representation at the conference, which is cool since this is the biggest conference in the field. We four presented one posters each, and I also had one with prof George Verghese from MIT. Here are links to the posters: 1,2, 3, 4, 5.

– On the way back I stayed a few days in Boston, and worked together with George Verghese on join matters. I also visited some other groups, and gave a guest lecture at Merrimack, which is a very cool company since they have almost completely integrated System Biology in their drug and anti-body development pipeline.

That’s all for now – please check in again later and see how our work and home page is progressing!

Gunnar