The ISBGroup Blog

In 2016/05/31, students who take the course TBMT19/33/37 and some members in ISB group went to AstraZeneca for a study visit. Four groups of students gave the final presentations for their project work. The presentations were interesting and successful. The topics of those projects vary from T2D cell level: signalling in fat and brain cells; the dynamics of glucose, insulin, fatty acid in whole level with relative drug simulation; the combination model of T-cell, mechanistic core, Lasso-omics and the study on brain activity by using fMRI.

After the students’ presentations, the project leader in AstraZeneca provided an lively introduction to their work, going through all the necessary steps and digging into details such as time cost and potential problems. That presentation really gave all the people a straight forward look at the working flow of real pharmacy modelling simulation.

Linnea Bergenholm and David Janzén, also some students who did their thesis in ISBgroup, who were students from Liu and now working in AstraZeneca shared their experience with attendants later. The topics included study period in Liu, further education and research and current work. The speech was inspiring since their past experience could be the tomorrow for the students.

During the lunch time, all people had the chance to sit together and exchange information with each other in a relaxing way, not only the students but also some staff who work in AstraZeneca.

Except for the presentations, students also made posters for their project which were used later in the afternoon for everyone to read. Meanwhile, many questions were raised from the people who attending the presentation. Every student in relative groups was trying to answer those questions from different perspectives which gives the audience a better understanding of the project. Opposition part was also held in the afternoon, where one group of student opposed against one other group. The opposition went really well and it was helpful for the students to find the drawback of their work.

For every group that attended the presentation, a logo is required for their project and the ‘best logo’ winner who got a cup was voted by the audience. And this year, group IntraCell won the honer.

The study visit to AstraZeneca gave students a chance to present their working results to those professional people and undergo the atmosphere in a company which has a tight connection to their study.

Almedalen is Sweden’s without a doubt biggest socio-political event. All of Sweden’s top politician’s are there, as are all major media, and most activist groups, and many generally engaged citizen. We are therefore proud to announce that ISBgroup this year will feature at this event. Our participation happens between 9-10AM on July 4, in Kinbergs plats 8, when we will give one of the introductory backgrounds as one member in the expert panel on research without test animals. (more info here) I, Gunnar, who will be the one participating, am looking much forward to this chance to visit this exciting event for the first time, to be able to attend many other interesting lectures, to meet and discuss with interesting, engaged, and influential people, and to be a part of some interesting on-stage discussions following my lecture.

If you are in Almedalen at the 2016 edition, come check us out! 🙂
/Gunnar

Spara

We have been invited to give an oral presentation at the annual systems and synthetic biology conference BioSynSys, which this year is held in Bordeaux, June 27-29. The lecture of Gunnar Cedersund will be held on June 29, and will be on recent conceptual and methodological developments that help us to find more accurate and well-identified predictions and prediction uncertainties, especially in the case of unidentifiability of parameters and single-cell data. Full abstract and title is appended below, and the conference home page is found here.

TITLE AND ABSTRACT

Prediction
uncertainty in the case of unidentifiability and single-cell data – new
concepts and methods

Mathematical
modelling is an integral part of both systems and synthetic biology, because it
can more accurately deal with the complexity of biological data. However, to be
truly useful, the predictions of the model must be in the form of core
predictions, i.e. they must come with a correct uncertainty. In the last few
years, there have been important progress in this field, especially concerning
the important situations of unidentifiable parameters and single-cell data.
This presentation will give an overview of some of these developments.

In the case
of unidentifiable parameters, it has become clear that traditional approaches
based on sensitivity analyses, the Hessian of the cost function, and
sampling-based Monte Carlo approaches all give inaccurate results. In such
situations, one may instead use rediscovered and recently improved alternatives
based on the conditional profile of the likelihood function. Importantly, these
methods can now not only be used for assessing the uncertainty of parameter
values, but for the uncertainty of arbitrary model predictions.

For the
case of single-cell data, problems with unidentifiability are often more
severe: it is often not possible to generate enough data from a single cell,
and averages over many cells provide inaccurate results. In such cases, it is
instead better to use methods from nonlinear mixed-effects modelling (NLME),
which borrows information across the entire cell-population. Using simulated
data where the truth is known, and real data from individual yeast cells, I
will illustrate when, why, and how NLME is advantageous.

All in all,
these new and improved concepts and methods provide important tools for a sound
and correct model-based analysis of single-cell data.

In Linköping, we have a quite rare scientific conference: a conference that has been arranged for over 20 years exclusively by undergraduate students! This conference is called KVIT, and it is arranged by the students in the cognitive sciences programme. The overall focus of the conference is the fascinating mix that is cognitive science: neurophysiology, psychology, IT, artificial intelligence, decision-support, user-interfaces, etc. The specific theme of this year was “Quality of life”, and at this conference we had been invited to give an oral presentation. This presentation was a bit unique because it for the first time outlined some less known long-term plans of our group: to merge and extend our research on a multi-level systems-level understanding of the brain based on mathematical modelling, with fundamental research on the relationship between quantum mechanics and possibilities for free will, and with research on different states of consciousness, such as sleep, narcolepsy, and different types of meditation.

Abstract is appended below, and the entire programme and more information of the conference can be found at the conference home page.

Abstract
One of the big promises of the Information Age is that of systems medicine: that our rapidly growing biomedical datasets will be possible to analyze using
advanced mathematical models, to produce things like automated
diagnoses, personalized treatments, and an improved drug and medical
device development. In this talk, I will go through some recent
developments in this field, to show that this promise is not a
far-fetched, science fiction utopia, but a rapidly approaching reality.
Focusing essentially on my own research, I will show how such
mathematical models now can be used to e.g. replace test animals when
developing new treatments for diabetes, and be used to better unravel
the complexity of the human brain. Using such tools, we can therefore
start to obtain a new type of holistic understanding of the human
organism, into which peces of knowledge both can be examined more
correctly, and subsequently be integrated into a useful picture of the
whole. I will therefore end by a comparison of this increasingly
holistic understanding with such found in e.g. yoga traditions for
thousands of years. What are the similarities and differences, and what
will it take to one day merge such understandings?

In the last week, we arranged a 2-day workshop on Biomedical engineering and decision-support. This workshop featured around 20 speakers and 30 attendees, from a wide variety of backgrounds. These backgrounds include all the steps involved in creation of decision-support systems (new biosensors, patient and personal health records, mathematical models, and the creation of usable interfaces), the testing and implementation of such systems (user-experience and user-groups, social scientists, health economy, implementation science, service design, and clinical end-users), and people from medical pedagogics, companies, and clinical decision-makers. This workshop was intended as a step towards further advancing the second-round of three already submitted VINNOVA applications (still pending), and – more generally – as a step towards the creation of a Linköping-based centre on Biomedical engineering and decision-support. This endeavor is open, so if you are interested in this process, send an email to either of the two arrangers: Elisabet or Gunnar Cedersund (elisabet.cedersund@liu.se and gunnar.cedersund@liu.se)

Some more information can be found at the workshop home page.

We have had an abstract selected for an oral
presentation at the 6th Conference
on Systems Biology of Mammalian Cells in Munich. The abstract is about our
long-term work with diabetes modeling. Gunnar will hold the presentation April
8th in the session Systems Medicine &
Systems Pharmacology chaired by Werner Mewes & Frank
Lammert. We hope to see you there!

On June 1, our annual project course – the Bachelor’s course for the ~30 students in Engineering Biology, TBMT33 – is having its final presentation day. This is a good chance to get a quick overview of existing projects within ISBgroup, and to see some of the different ways that mathematical modelling can be used as an integrated tool in experimental and clinical research. The schedule of the day is as follows.

All presentations in Linden, Campus US
8.15-9: Master Thesis presentation, “Quantitative translation of drugs’ effects on type 2 diabetes mellitus: from diabetic rodent models to patients”, Philip Blomström. Supervisors: Elin Nyman and Monika Sundqvist, Project done at AstraZeneca

9.15-9.45 “Intracellular insulin signalling and mechanisms of adiponectin release”. Supervisor: Rasmus Magnusson. Collaborating groups: Peter Strålfors (IKE), Cecilia Brännmark (Gothenburg Univ).
9.45-10.15 “Improvement of a Mathematical Liver Model for Diagnosis and Surgical Planning”, Supervisor: Markus Karlsson. Collaborating group: Peter Lundberg (IMH/CMIV)

10.15-10.30 Break

10.15-10.45 “Multi-level and multi-time scale modelling of glucose homeostasis disorders: monitoring in ICU and obesity drug simulations”
Supervisor: Andrea Hjelm. Collaborating groups: Peter Strålfors (IKE), Peter Gennemark (AstraZeneca), Folke Sjöberg (IKE)

10.45-11.15 “Modelling the BOLD response in fMRI”
Supervisor: Karin Lundengård. Collaborating group: Maria Engström (IMH/CMIV), Fredrik Elinder (IKE)

11.15-11.45 “Understanding desensitization – by examining cardiac myocytes and sensory neurons”
Supervisors: William Lövfors and Rikard Johansson. Collaborating groups: Jordi Altimiras (IFM), Claudio Altafini (ISY)

12-13 Poster presentations of all projects outside of Berzelius.

Questions and more info: Gunnar Cedersund, gunnar.cedersund@liu.se

Welcome! 🙂

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!