The ISBGroup Blog

We are now in the middle of preparing for (hopefully) four workshops to take place here in Linköping in the period of June 17-23.

One of the reasons for these workshops is that we want to make use of our newly recruited guest professors Hiroaki Kitano and Jens Timmer, by having some of the most important international players come here and discuss some vital issues with us. Kitano is one of the world-leading players in model construction (e.g. by being the founder of CellDesigner, the most widely used software in the field), and he has also recently moved into hierarchical modelling, which is the topic of one of the workshops. Similarly, Jens Timmer heads one of the leading groups of sound data-analysis approaches to systems biology modelling, including the handling of uncertainty in data; this is the topic of another workshop. The third workshop comes from a network that we are forming on multi-level hierarchical modelling of type 2 diabetes, and the final workshop is meant for us in the Linköping Centre for Systems Biology.

More information on all these workshops can be found here

So, welcome to Linköping in June! 🙂

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.

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.