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The ISBGroup Blog

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

New Article: Digital twin predicting diet response before and after long-term fasting

Uncategorised Posted on Mon, September 26, 2022 14:30:55

Read our new article published in PLoS Computational Biology!

You find the full link here:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010469

Silfvergren O, Simonsson C, Ekstedt M, Lundberg P, Gennemark P, Cedersund G. Digital twin predicting diet response before and after long-term fasting. PLoS Comput Biol. 2022 Sep 12;18(9):e1010469. doi: 10.1371/journal.pcbi.1010469.

ABSTRACT

“Fasting and diet are central components of prevention against cardiovascular disease. Unfortunately, there is little consensus regarding which diet schemes are optimal. This is partially because different clinical studies contribute with different non-connected pieces of knowledge, which have not been fully integrated into a useful and interconnected big picture. In principle, mathematical models describing meal responses could be used for such an integration. However, today’s models still lack critical mechanisms, such as protein metabolism and a dynamic glycogen regulation. Herein, we present a) a new expanded model structure including these mechanisms; b) a set of parameters which can simultaneously describe a wide array of complementary estimation data, in both healthy and diabetic populations; c) a personalisation-script, which allows these generic parameters to be tuned to an individual/sub-population, using demographics (age, weight, height, diabetes status) and historic metabolic data. We exemplify how this personalisation can be used to predict new independent data, including a new clinical study, where a qualitatively new prediction is validated: that an oral protein tolerance test gives a clear response in plasma glucose, after, but not before, a 48h fasting period. Our combined model, parameters, and fitting script lay the foundation for an offline digital twin.”



A multi-data based quantitative model for the neurovascular coupling in the brain

Uncategorised Posted on Thu, September 08, 2022 20:06:18

A while back we made our expanded brain model, capable of describing and predicting various multi-species data, available on bioRxiv (https://doi.org/10.1101/2021.03.25.437053). After some further work we are aiming to submit our work, In the meanwhile feel free to take part of the currently available version.

Abstract: The neurovascular coupling (NVC) forms the foundation for functional imaging techniques of the brain, since NVC connects neural activity with observable hemodynamic changes. Many aspects of the NVC have been studied both experimentally and with mathematical models: various combinations of blood volume and flow, electrical activity, oxygen saturation measures, blood oxygenation level-dependent (BOLD) response, and optogenetics have been measured and modeled in rodents, primates, or humans. We now present a first inter-connected mathematical model that describes all such data types simultaneously. The model can predict independent validation data not used for training. Using simulations, we show for example how complex bimodal behaviors appear upon stimulation. These simulations thus demonstrate how our new quantitative model, incorporating most of the core aspects of the NVC, can be used to mechanistically explain each of its constituent datasets.

Overview of the presented study: A: Cellular pathways underlying the neurovascular coupling (NVC). B. Overview of commonly used experimental techniques C. Overview of the study D. Comparison of different published models describing the NVC with regards to different mechanisms


VPH 2022 – Less than 2 weeks to the conference! 6-9 September, Porto, Portugal  

Uncategorised Posted on Thu, August 25, 2022 16:41:59

Dont miss the chance to meet us at The Virtual Physiologiacl Human Conference 2022!

We have three presentations and our digital twin will be a part of the welcome reception

Dancing Digital Twins performance

Welcome reception, 7th September, 19:30 Auditorium

Unique collaboration between the Swedish researcher and pianist Gunnar Cedersund and choreographer and dancer Julia Bengtsson fuses digital twin technology and visualization with dance and music

Nicolas Sundqvist

Presentation, 8th September

Session 14: Multiscale modelling. 8.30-10.30, Room 2

An interconnected multi-level mechanistic model of the human brain

Oscar Arrestam

Presentation, 9th September

Session 22: Computational modeling in health and disease 4. 8.45-10.15 Room 2

Digital twin predicting diet response before and after long-term fasting (see poster below)

Gunnar Cedersund

Presentation, 9th September

Session 25: Computational tools and simulation in biomechanics 4

10.30-12.30 Auditorium

M4-health: digital twins that follow you throughout your health journey



Uncategorised Posted on Mon, June 14, 2021 11:36:20

Nu är programmet för Almedalen ute, och vi kommer att dyka upp i diskussioner kring den Digitala Tvillingen på måndag den 5 juli kl 13.15-14.00. Missa inte! Konferensen är digital så du kan se den bekvämt hemifrån soffan.

https://eastsweden.se/almedalen



Programmer wanted!

Uncategorised Posted on Tue, May 25, 2021 11:30:31

We are looking for a programmer to work on the interface for the digital twin project. Please spread to anyone you think would be a good match!

Ansök här / Apply here

Here is a short film about the Digital Twin project.

Our work with the new digital twin technology – an interactive computer model, describing the multi-organ, and multi-timescale biochemistry and physiology of a specific person – has now led to a first prototype which is almost ready to be tested in a clinical environment. However, to be able to do that, we need to have suitable user interface, and this is where you come in!

In english:

“We are looking for someone experienced in working with programming, visualisation, software architecture, and user friendliness. Submitting a sample of previous work with you application will increase your chances, in particular apps and software projects that includes visualisation. You are interested in design and you are an attentive listener who can work in a group setting to interpret the best solution to what researchers, clinical personnel and private users need.

Your tasks will primarily be development of the front-end software for research and clinical environments, focusing on visualisation and app-design. ISB group at IMT have developed a so called Digital Twin, computer model copies of a patient, which will function as support for the Health Conversation. We have a few previously developed prototypes, but now we need someone to help us make a version with a user interface suitable for testing in clinical studies. You will work mostly with the coding of the software, but some design and user interaction and evaluation is also included.”

På svenska:

“Vi söker nu någon som har erfarenhet av att arbeta med programmering, visualisering, mjukvaruarkitetktur och användarvänlighet.  Tidigare arbetsprov av egna utvecklade appar och andra mjukvaruprojekt, speciellt sådana som inkluderar en visualiseringskomponent, är en viktig del av bedömningen. Du är antagligen intresserad av design och en god lyssnare som kan arbeta i grupp och tolka vad både forskare, vårdpersonal och privata användare behöver. 

Dina arbetsuppgifter kommer bestå i framför allt arbete med att utveckla front-end mjukvara för en vetenskaplig och klinisk miljö, med fokus på visualisering och app-design. I ISB-group på IMT har vi utvecklat en så kallad Digital Tvilling, datorkopior av en patient, som ska fungera som stöd i vårdens hälsosamtal. Vi har tidigare utvecklat ett par prototyper, men behöver nu någon som gör en första mer färdig version av användargränssnittet att testa i kliniska studier.  Du kommer att arbeta mycket med själva kodningen av mjukvaran, men en del design och användarinteraktion ingår också. “

If you have any questions, please contact Karin Lundengård at karin.lundengard@liu.se



New postdoc position in the new 12 MEuro X-HiDE project

Uncategorised Posted on Sun, August 30, 2020 01:17:35

There is a now a first postdoc position open in the new X-HiDE project, of which we are a central part. X-HiDE is a new major systems biology center that is about to launch in Sweden, which recently got a major grant of 12 MEuro, over an 8 year period. The topic will be systems biology of immunology. The over-arching goal is to build up a comprehensive and re-usable model, to be useful as a module in other models for a wide variety of diseases associated with dysfunctional inflammation: cardiovascular disease, auto-immune diseases, NASH, COPD, diabetes, cancer, etc. There are more than 10 experimental and clinical partners on board, which all will contribute with data and biological/medical expertise. Apart from this, a number of large and small companies are on board as co-funders, including e.g. AstraZeneca, and Wolfram MathCore. This particular postdoc is focused on modelling, and the main expertise sought after is data-driven mechanistic modelling (typically done using ODEs).

Because of the existence of the long-term substantial funding, there will be more similar modelling positions opened up later, including a soon to be announced more senior tenure-track position. These early positions will be excellent opportunities for junior researchers, who want to be a part of building up a new systems biology center.

NOTE: Deadline for this first postdoc position is midnight September 1 CEST!

/Gunnar Cedersund, leader of X-HiDE’s workpackage on modelling



New students!

Uncategorised Posted on Tue, April 14, 2020 14:02:36

We have several master-thesis and internship students working in our group this spring. Here is a small introduction!

Gustav Magnusson

I’m a master student in Physics with a hope to contribute something to the world of Systems Biology. The aim of my master thesis is to work with the Digital Twin, to put together the various models produced here at ISB to form an interface for users such as patient and researchers to test various situations and hypothesis. The goal is also to work on my own model which could be a part of the Digital Twin, perhaps with focus towards phyisical training, atherosclerosis or the immune system.

Lucas Raihle
Hi! I’m Lucas and I will be interning at ISB group during March-September. My project will revolve around making a model that can describe how diet affects the progression of NAFLD (non-alcoholic fatty liver disease). NAFLD is the most common liver disease in the world and is heavily correlated with the metabolic syndrome. Understanding the progression of NAFLD could lead to more effective forms of treatment and diagnosing. I’m happy to join this group and excited to start my project.

Johanna Hansson
Hi, my name is Johanna Hansson and I have just started an internship at ISB group. I will be working on a project to describe the disease progression of atherosclerosis to stroke and how the consequential oxygen loss affects the brain function. First, I will develop a mechanistic atherosclerosis model and later connect it with existing models of e.g. blood flow and stroke. Understanding atherosclerosis and its relationship with stroke could help predict who is at risk of having one. With that knowledge, we may be able to prevent the stroke from happening and save lives. I will work on my project for 6 months and I am excited to see the result!

Jonatan Baggman
Hi! My name is Jonatan and I’m doing my master thesis here at ISB group this spring. For my master thesis I’m looking into imputations for the Digital Twin, how to estimate the input values which are not measured directly from the patient. I will look into different methods of imputation and will compare these. Hopefully, I will be able to present how to make the Digital Twin personalized without measuring all values from the patient!



More grants to Systems Biology in Linköping

Uncategorised Posted on Thu, November 28, 2019 16:36:06

Elin has received two substantial grants, from the Swedish Research Council (VR) and from the Center for Industrial Information Technology (CENIIT). Both grants are given to young and promising researchers.

VR-NT From omics to patient specific simulations (950 000 SEK per year for 4 years)
CENIIT Executable models for drug development (450 000 SEK per year for up to 6 years)



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