The ISBGroup Blog

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The ISB group.

Today Zaheer Ali, who has been working in our group since spring 2012, presented and defended his work.

The title was Mathematical Modeling of Electrophysiological Data of Facilitation in Layer 6 Pyramidal Cells (abstract below).

Abstract:

Facilitation is a distinctive activation pattern shown by pyramidal
cells in the layer 6 of the cerebral cortex upon rapid and repeated stimulations.
This behavior leads to the generation of tonic-clonic seizures which is a
defining feature of epilepsy. Patch-clamp recording techniques performed on
these cells show facilitation in different experiments. A mathematical modeling
approach is used in order to find the possible mechanism of facilitation
depending on different calcium domains in the presynaptic neurons. Four
different versions of the model have been constructed using ODEs. First version
of the model is a simple model of three compartments in the presynaptic neuron
with an influx of calcium at the triggering calcium compartment, the buffer
compartment and the stable internal domain of calcium can describe the data of
facilitation. Second version of the model has the calcium influx through a
micro-domain compartment near the cell membrane because of physical distance
between ion channel and the vesicle, in addition to the three compartments. The
third version of the model has a limited calcium buffer without micro-domain
calcium compartment which provides saturation to the buffer in this model and
the final version of the model is similar to third version of the model with
the addition of a micro-domain calcium influx. All models can describe the
experimental data sets of facilitation separately fitted to the model. In
addition, the third version of the model can describe all the experimental data
at the same time qualitatively.

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.