The ISBGroup Blog

The ISBGroup Blog

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Here you can read about everything that's happening in the ISB Group.

New student - Thea

NewsPosted by ISB Group Mon, October 16, 2017 15:41:04
This autumn, we welcome another new student in our group: Thea Sandqvist


My name is Thea and I'm here in the ISB Group to do a project in systems biology for my 6th semester in Medicine.

My project is about insulin- and glucose metabolism in rodents switching between chow- and high fatty based-diets. The project is based on a multi-level-multi-scale model conducted by former ISB Group-member Niclas Berqqvist. My experimental data comes from Karin G. Stenkula and her research group in Lund.

Besides spending time at the office I enjoy an occational pain-au-chocolat (or two or five).

Nailing of thesis on Friday the 13th

NewsPosted by Rikard Johansson Thu, October 12, 2017 20:48:59
This Wednesday I nailed my thesis outside the C2 lecture hall at campus Valla. It was a peaceful, quiet and beautiful ceremony.

Tomorrow, Friday the 13th, I will nail a second copy at IMT, with a bit more pomp and circumstance.
Welcome to "spika-fika" at 14.45 at IMT, campus HU if you want to join for some cake.

You can find my thesis online:

New student!

NewsPosted by ISB Group Thu, September 21, 2017 09:38:29

This autumn, we welcome a new student in our group: Valentin Kindesjö

​Hello! My name is Valentin Kindesjö. I started medical school at Linköping University in the spring of 2015 after studying a year and a half of biomedical engineering. For the autumn of 2017, I have found my way back to IMT to join ISB group for a project in mathematical modelling, where I will be continuing the work of previous students (most recently Johanna Fridberger and Thirza Poot) in expanding a multi-level model over the regulation of glucose, insulin and fatty acids, created by joining a glucose- and insulin model created by Dalla Man et al and a NEFA model, created by Jelic et al as an expansion on a model by Fianne Sips. I will be working to make the NEFA part of this model more physiologically correct. Hopefully, this work will bring us closer to finding out the exact role played by adipose tissue in maintaining the systemic energy homeostasis, and shed some light over the dynamic interplay between the different mechanism involved in the storage and release of fatty acids.

I am spending my autumn in Oxford, at the group of Fredrik Karpe, professor of metabolic medicine at the Oxford Centre for Diabetes, Endocrinology and Metabolism, who conducted the experiments where the data I will be using was collected.

Fredrik Eklund presented his thesis, Bayesian networks for CVD Prediction, and continues with ISB Group

NewsPosted by Fredrik Eklund Wed, September 06, 2017 16:41:25
Cardiovascular disease (CVD) is one of the most life-threatening conditions of our time and one with limited treatment options for severe cases. Improved diagnostics and preemptive treatment methods are thus especially important. Fredrik Eklund’s thesis, labelled “Guided Bayesian Graphical Network model for Cardiovascular Disease Prediction”, continues the work towards a tool aimed to provide decision support for medical practitioners.

Bayesian Graphical Networks (BGNs) are prominent decision components in the field of machine learning and artificial intelligence. A strength lies in their ability to infer partially missing data using its distribution and other data, i.e. from the same patient. This is a powerful feature in clinical practice because some informative measurements may be costly or invasive to obtain.
The thesis report suggests rules to model BGNs by in order to battle issues with high dimension clinical data as well as to reflect the pathophysiology of CVD. An algorithm was then developed to build BGNs according to these rules. Following these two steps, a BGN to predict CVD was built from clinical data on type 2 diabetes patients. The result is a network which joins prior knowledge with machine learning techniques. The network can be considered a proof of concept and a mild success.
According to agreement with Gunnar Cedersund, Fredrik Eklund will continue work on the model in the months to come.

New M.Sc thesis presentation: Niclas presented his work about multi-level and multi-scale modelling in rodents

NewsPosted by Niclas Bergqvist Fri, June 16, 2017 13:05:24

Last Wednesday (14/6) I presented my master thesis entitled Multi-level and Multi-scale Modelling: From Adipose Intracellular Insulin Signaling to Whole Body Metabolism and Weight Alteration. This presentation included a brief explanation of all my work here as a part of ISBGroup. I started my journey here as an intern already in the summer of 2015 following the bachelor course. Back then, I worked with a project involving the development of a model describing the intracellular signalling chain in rat adipocytes. The internship lasted for two months, but the project went so well, that I decided to continue the work alongside my studies. One and a half year after the start of the internship, the project successfully resulted in a published article. Around that time, I was supposed to start writing my master thesis, so it felt natural to continue on this track. So, by using the newly developed intracellular model as a base, I continued the development towards a first multi-level and multi-scale model in rodents. The abstract from my master thesis is attached below.

Type 2 diabetes, T2D, is a prevalent, costly disease that affects millions of people worldwide. It is a complex metabolic disorder which is characterized by insulin resistance. The resistance is believed to initially arise from adipose intracellular malfunctions and later spread to adjacent tissues, eventually affecting mechanisms on multiple body levels. To handle this complexity, mathematical models has been developed through systems biology modeling. These include models, in both rodents and humans, that describe mechanisms on single body levels, as well as more advanced models that describe T2D associated mechanisms on multiple levels. However, these multi-level models have so far mainly revolved around humans, and no such model focused around diabetes in rodents has yet been developed. Animal models possess many benefits, like processing valuable animal data that is difficult to obtain from human experiments, or act as replacement for test-animals. For these reasons, a first multi-level and multi-scale rodent model has been developed that describe mechanisms on multiple levels; from the intracellular level (the adipose insulin signaling chain from the insulin receptor, IR, to the GLUT4 transporter) to the whole-body level (including the glucose-insulin metabolism and weight change). Experimental data was obtained on these various levels, and used to improve and test the model. The intracellular section of the model was created through a connection of two existing models and can describe over 140 experimental data points. It was also validated with independent experimental data and was used to form predictions about the relative contribution of the pathways from IR to GLUT4. The new multi-level model was developed after new connections was established between this intracellular model and a model describing meal responses over a couple of hours, as well as with a model describing weight change over days and weeks. The resulting multi-level model have created insights to what mechanisms are necessary in order to simulate data on all levels. The model also aims to increase the mechanistic understanding of T2D and eventually provide a contribution to the drug development process, by reducing the amount of animal trials and increasing the success chance of the developed drugs.

- Niclas Bergqvist

ISBgroup goes to Almedalen

EventsPosted by Karin Lundengård Wed, May 10, 2017 23:41:38
As part of the collaboration with ”Forska Utan Djurförsök” (The Swedish Fund for Research without Animal Experiments), ISB group is going to Almedalen in July. Almedalen is the biggest political event of the year in Sweden, and Gunnar Cedersund has been invited to participate in two events:

* Monday July 3, 13-14.30 in Maltfabriken. Then Gunnar and a few others will give short initial presentations, followed by a panel debate with politicians, and ended with some hands-on tutorials, by some of the students from ISBgroup. If you want to try to simulate our own models for diabetes, you should come then. (link to more info)

* Thursday July 6, 10-11.30 in Maltfabriken. Then a short introduction will be followed by a longer session with hands-on testing, not only regarding mathematical models but also regarding other experimental alternatives to animal experiments. The focus then is on chemicals and cosmetics testing (involving e.g. the qsar model). (more info)

Apart from these two events, Forska utan djurförsök will also have a final opportunity to come and talk with them on Friday July 7, at 10-11.30 in Maltfabriken. This will be a more informal event, with the opportunity to come and talk and have coffee with people who know a lot about these issues (link).

Karin for ISBgroup

May 11-12, Workshop on biological modelling at LiU

EventsPosted by Gunnar Cedersund Mon, May 08, 2017 18:21:50
There is a workshop upcoming about modelling of biological systems at Linköping university. It will take place Thursday-Friday this week, May 11-12, 2017, and is open to everybody who wants to attend: students, scientists, and the general public. We will contribute with one presentation, at Thursday 16-16.20. This presentation will consist of an overview of our modelling philosphy and of our various modelling projects. Apart from us there will be some 20-25 other groups who will present as well. Almost all of the presenters either still work, or have worked, at LiU, i.e. Linköping university.

More information about the workshop can be found here.

Ph.D. defense of Mikael Forsgren, May 23

EventsPosted by Gunnar Cedersund Mon, May 08, 2017 13:32:25

Last Friday, one of our Ph.D. students - Mikael Forsgren - nailed up his Ph.D. thesis on our local thesis tree. He thus followed in the footsteps of many many others, ranging back possibly even beyond Martin Luther, by thus publically announcing that he has something that he would like to publically discuss: the thoughts and results in his thesis.

The formal defense will be held at 13.15 in Eken, at HU, Linköping, Sweden. The opponent will be Stephen Sourbron, from Leeds, who is an expert on perfusion modelling in different organs. Mikael's thesis is about modelling of not only perfusion, but also of intracellular uptake and release, concerning the contrast agent Primovist. He shows how the estimation of such uptake properties using mechanistic modelling can be used to obtain new patient-specific biomarkers, which can be obtained from MRI examinations, and which thus can move to eventually become a non-invasive replacement for today's invasive liver biopsy examinations. The goal is that this should lead to a reduction in healthcare cost and individual suffering, and to an increase in accuracy and diagnostic power.


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