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The ISBGroup Blog

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

Nailing of thesis on Friday the 13th

News Posted on 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:

Two new summer students

News Posted on Wed, July 06, 2016 15:57:34

Two new students are joining us this summer. Here is their introduction:



Our names
are Erik and Martin and we are working here at the ISB-group over the summer.
We thought that it might be appropriate to tell you about who we are, and what
we are working with!

We are both
students here at Linköping University, studying engineering in biotechnology. We
have both just finished our third year and completed our Bachelor’s project
together under the supervision of Gunnar.

During the
summer, we will continue with the bachelor’s project in cooperation with
AstraZeneca. The project revolves around creating and evaluating a mathematical
model over how the maturation of macrophages can be regulated, and throughout
this, be able to control the immune response in the immune system. If we were
able to control the immune response we could for example limit the symptoms of
auto immune diseases, in which there usually is a too high pro inflammatory

Bachelor’s course

News Posted on Fri, February 12, 2016 13:45:00

For the
last couple of years the students in Engineering Biology (TB) have done their bachelor’s
projects under our supervision. This year is no different! Right now the
students are finishing phase 1, where they are learning about systems biology
and how to implement, optimize, and analyze models. They are also right now
meeting their customers for the projects they will start on later this spring.

This year
we have four exciting projects. In the first project, the students will attempt
to unravel new insights of intracellular signaling in different tissues. They
will at the same time attempt to bridge the understandings of insulin signaling
with adrenergic signaling. The end-goal is to gain new knowledge of metabolic
and cardiovascular diseases.

In the
second project, the insulin-glucose dynamics at the whole-body level is the
focus. Three subgroups will work with variating glucose levels in the Intensive
Care Unit (ICU), the interplay between insulin, glucose and NEFA, and the long term
effects of antioxidants respectively.

In the third project, five students will work together to understand
important aspects of the immune system. By modeling both the transcription of
genes within T-cells, and by bench marking the algorithms to do so, important
aspects of diseases, e.g. allergy, can be explained. This work is
potentially important in a wide variety of applications, both for drug
development, diagnosis, and for understanding of the pathology involved in a
wide variety of diseases.

In final
project, five students will work in a combined effort to further improve the
current understanding of the fMRI-BOLD response and its underlying neurovascular coupling.
They will contribute towards explaining current research questions such as
blood flow regulation in ischemia patients, neural metabolism and potential
bio-markers for brain function. By this, we aim towards bridging the gap
between our modelling efforts and future clinical applications.

These projects
have been started already now but will take on full speed during the second
half of the spring. Three times the students will present their ongoing
findings, and during the final presentation this spring one group might find
themselves the winner of the yearly logo-competition.

Last years winners of the prestigeous trophy: “Improvement of a Mathematical Liver Model for Diagnosis and Surgical Planning”

Kicking off the new year

News Posted on Mon, February 02, 2015 16:50:22

2015 looks like it is going to be a good year for us, starting with two publications:

* Dominant negative inhibition data should be analyzed using mathematical modeling – re-interpreting data from insulin signaling.

* Mathematical modeling improves EC50 estimations from classical dose-response curves.

We celebrated this and the start of the new year with an after work kick off at De Klomp in Linköping

ISB Group at after work at De Klomp. January 2015.

6th Swedish Meeting on Mathematics in Biology

Events Posted on Wed, December 03, 2014 10:58:06

On Thursday and Friday, the 6th Swedish Meeting on Mathematics in Biology takes place in Linköping.

We will be there and do a small presentation of our work. Hope to see you there!

A letter from Boston

News Posted on Mon, February 25, 2013 13:20:17

Here comes a few words from Linnea and David, two members of
the ISBgroup in Linkoping.

We are both currently living in Boston, USA,
experiencing systems biology in an industrial environment.

We are doing internships as modelers at Merrimack
Pharmaceuticals, a biopharmaceutical company focused on cancer drug development
using network biology. Linnea’s project involves mechanistic modeling of the
DNA damage response pathway, aiming at identifying possible synergistic drug
combinations. David’s project concerns PKPD-modeling of an in-house drug which
currently is in the end of its pre-clinical phase.

One month into our
internships, we have experienced long and intense work days, learned about the
company and its pipeline, lasted through a “monster blizzard”, and met a lot of
talented people from all over the world.

Linnea Bergenholm and David Janzen at Merrimack
Pharmaceuticals, Boston.

Master Thesis Presentation: Linnea Bergenholm

Events Posted on Fri, February 22, 2013 14:50:59

Right before christmas, Linnea Bergenholm presented her master thesis Modeling as a Tool to Support Self-Management of Type 1 Diabetes. This thesis work was done in our group, collaborating with the companies Linkura and Wolfram Mathcore, aiming to develop and investigate dosing tools for diabetics.

You can download the thesis here


1 diabetes (T1D) is an auto-immune disease characterized by
insulin-deficiency. Insulin is a metabolic hormone that is involved in
lowering blood glucose (BG) levels in order to control BG level to a
tight range. In T1D this glycemic control is lost, causing chronic
hyperglycemia (excess glucose in blood stream). Chronic hyperglycemia
damages vital tissues. Therefore, glycemic control must be restored.

common therapy for restoring glycemic control is intensive insulin
therapy, where the missing insulin is replaced with regular insulin
injections. When dosing this compensatory insulin many factors that
affect glucose metabolism must be considered. Linkura is a company that
has developed tools for monitoring the most important factors, which are
meals and exercise. In the Linkura meal and exercise tools, the
nutrition content in meals and the calorie consumption during exercise
are estimated. Another tool designed to aid control of BG is the bolus
calculator. Bolus calculators use input of BG level, carbohydrate
intake, and insulin history to estimate insulin need. The accuracy of
these insulin bolus calculations suffer from two problems. First, errors
occur when users inaccurately estimate the carbohydrate content in
meals. Second, exercise is not included in bolus calculations. To reduce
these problems, it was suggested that the Linkura web tools could be
utilized in combination with a bolus calculator.

For this purpose,
a bolus calculator was developed. The bolus calculator was based on
existing models that utilize clinical parameters to relate changes in BG
levels to meals, insulin, and exercise stimulations. The bolus
calculator was evaluated using data collected from Linkura’s web tools.
The collected data showed some inconsistencies which cannot be explained
by any model. The performance of the bolus calculator in predicting BG
levels using general equations to derive the clinical parameters was
inadequate. Performance was increased by adopting an update-algorithm
where the clinical parameters were updated daily using previous data.
Still, better model performance is prefered for use in a bolus

The results show potential in developing bolus
calculator tools combined with the Linkura tools. For such bolus
calculator, further evaluation on modeling long-term exercise and
additional safety features minimizing risk of hypoglycemia are required.

Autumn Kick-Off

Social Events Posted on Tue, October 23, 2012 15:26:26

Better late than never! That’s unofficial motto of the
ISB-group. Last week we had a get-together to celebrate the new semester.
We said goodbye to some of our members leaving the group and a big welcome to
our new students. Everyone brought their own contribution to create a veritable
buffet of delicious food… and there was much rejoicing!

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