The ISBGroup Blog

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.

The ISB group would like to extend a warm thank you to everyone who attended the SystemsBiology@LiU-day. We think that this day was a huge succes as an initial ice-breaker between the various groups at Liu which work with Systems Biology.

We are now working on setting up the mail-list we discussed. If you wish to be a part of the list, please send us a mail

Yet again, thank you, and if you missed the day, make sure to sign up to the mailing list in order to not miss out on any future events.

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The ISB group

Tomorrow (Wednesday, October 7th) Peter Nyberg presents his master thesis work “Evaluation of two Methods for Identifiability Testing”. A joint supervised project of our group, Division of Automatic Control at the Department of Electrical Engineering, and Mathcore. The presentation will take place at campus Valla, Glashuset (Building B, entrance 25) at 10:15.

Abstract:
This thesis concerns the identifiability issue; which, if any, parameters can be
deduced from the input and output behavior of the model? The two types of
identifiability concepts, a priori and practical, will be addressed and explained.
Two methods for identifiability testing are evaluated and the result shows that
the two methods work well if they are combined. The first method is for a priori
identifiability analysis and it can determine the a priori identifiability of a system
in polynomial time. The result from the method is probabilistic with a high
probability of correct answer. The other method takes the simulation approach to
determine whether the model is practically identifiable. Non-identifiable parameters
manifest itself as a functional relationship between the parameters and the
method uses transformations of the parameter estimates to conclude if the parameters
are linked. The two methods are verified on models with known identifiability
and then tested on some examples from system biology. Although the output from
one of the methods is cumbersome to interpret, the results show that the number
of parameters that can be determined in practice (practical identifiability) are
far fewer then the ones that can be determined in theory (a priori identifiability).
The reason for this is the lack of quality, noise and lack of excitation, of the
measurements.

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