SCHEDULE FOR PH.D. COURSE AND WORKSHOP NOV 26-DEC 6, 2012
Note that the below schedule still is preliminary. An updated version is available at
http://isbgroup.eu/2012/ where a map to IMT1, IMT2 & IMT10 can be found
Monday Nov 26: Basic introductions to modeling, day 1
10-12: Gunnar Cedersund, Introduction to systems biology, and to the course (IMT1)
Lunch
13.15-14.30: Option 1, Mikael Forsgren/Robert Palmér, MathCore Wolfram, Multi-level
modeling using Wolfram system modeler
13.15-15: Option 2, Gunnar Cedersund, Basics of formulating a model (TBA)
14.30-16: Computer room, getting started (IMT11)
16-17: Student presentations (IMT1)
Tuesday Nov 27: Basic introductions to modeling, day 2
9-10: Jacky Snoep, Cape Town, Modelling of metabolism: history, methods, examples (IMT1)
10-11: Options 1, Jacky Snoep, Cape Town, Modelling of metabolism: derivations of rate
expressions (IMT1)
11-12: Option 1, Maria Kjellsson, Uppsala, Nonlinear mixed effect modeling using NONMEM
(IMT2)
10-12: Option 2, Gunnar Cedersund, Basics of formulating and optimizing a model (IMT10)
Lunch
13.15-16: Hands-on session: basic introduction, NONMEM, System modeler, or own project
(IMT11)
16-17: Student presentation (IMT1)
Wednesday Nov 28: Modelling of diabetes, part 1, day 1
9-11: Gunnar Cedersund and Elin Nyman, Linköping, Towards a whole-body multi-level
model for type 2 diabetes: addition of an adipocyte module (IMT1)
11-12: Jacky Snoep, South Africa, Modelling of whole-body and red blood cell metabolism in
malaria (IMT1)
Lunch
13.15-16: Hands-on session, Cont from before and/or on adipocyte module (IMT11)
13.15-16: Tour to the cell biology lab
16-17 Student presentations (IMT1)
Thursday Nov 29: Modelling of diabetes, part 1, day 2
9-10: Folke Sjöberg, MD, Local in situ measurements and perturbations of glucose and
insulin using microdialysis (IMT1)
10-11: Britta Göbel, Sanofi, Germany, Modelling of brain regulation of whole-body glucose
homeostasis
11-12: Hands-on sessions and excursion to the labs – cont from day before (IMT11)
Lunch
13.15-15: Hands-on sessions and excursion to the labs – cont from day before (IMT11)
15-16: Peter Strålfors, Linköping, The adipocyte module: an experimentalist’s view
16-17: Student presentations (IMT1)
Friday Nov 30: Modelling of diabetes, part 1, day 3
9-13: Ph.D. defense of Cecilia Brännmark (Berzelius-salen)
14-15: Henning Schmidt, Novartis, Nonlinear mixed-effect modeling using Monolix with
models exported from the SBtoolbox2 (IMT2)
Saturday Dec 1: Workshop, Network approaches to systems medicine – in IMT1
09.00-09.30
An introduction to why networks can help to find diagnostic and therapeutic targets.
Mikael Benson, Linkoping University
09.30-10.10
Characterisation of T cell subset responses in peanut allergy using microarrays.
Victor Turcanu, King's College, London
10.10-10.25
Coffee break
10.25-11.05
Personalizing molecular and physiological phenotypes.
Andreas Beyer, Technische Universitat Dresden, Germany
11.05-11.45
Breast Cancer Molecular Networks.
Miguel Pujana, Institut d'Investigacio Biomedica de Bellvitge, Spain
11.45-13.00
Lunch
13.00-13.40
Application of systems approach in identification of cancer biomarkers.
Liung Wang, Medical College of Wisconsin, USA
13.40-14.20
Inference of microRNA-regulated gene networks and functions by co-expression analysis.
Sandro Banfi, Second University of Naples, Italy
14.20-14.35
Coffee break
14.35-15.15
Towards systematic analysis of metabolic fluxes in mammalian cells.
Roland Nilsson, Karolinska Institute, Stockholm
15.15-15.55
Studying protein network dynamics in health and disease.
Paola Picotti, Eidgenossische Technische Hochschule Zurich, Switzerland
15.55-
Group discussions*
19.30-
Dinner
* The group discussions will be based on specific questions. Those questions have been given
by the participants by email before the workshop or during the day. During the lunch break
we will pass around a list so that each participant can list her or himself in a group discussing
those specific questions (5-7 people in each group). Light snacks and beverages will be
available.
Day 2 – Workshop Day 2: Model-based approaches to systems medicine – in IMT1
09.00-09.15
Welcome to day 2 "Model-based approaches". Gunnar Cedersund
Morning session: Comparison of different tools for model-based diagnosis.
9.15-9.25 PKPD-modelling for medical diagnosis. Ron Keizer, Uppsala, Sweden.
9.25-9.45 Image-based modelling for medical diagnosis. Andrea Schenk, MEVIS Fraunhofer
Centre Bremen, Germany.
9.45-10.10 Medical decision analysis with probabilistic graphical models. Fransisco Javier
Diez, Madrid, Spain.
10.10-10.30 Merging of all of the above tools. Gunnar Cedersund, Linköping, Sweden.
10.30-11.00 Coffee
11.00-11.20 Data-Based Modeling and its Application to Neurology. Björn Schelter, Freiburg,
Germany.
11.20-11.40 The viewpoint of technical diagnosis. Mattias Krysander/Erik Frisk, Linköping,
Sweden.
11.40-12.00 General discussion on all the tools
12.00-13.30
Lunch
Afternoon session: Modelling for drug-development
13.30-13.45 Welcome to the afternoon session, Gunnar Cedersund, Linköping
13.45-14.15 Examples and showcases of modelling in drug-development, Balaji Agoram,
Medimmune, AZ, UK
14.15-14.45 Examples and showcases of modelling drug-development, Henning Schmidt,
Novartis. Switzerland
14.45-15.05 Modelling the effect of a drug on a population: should it be introduced into
clinical practice?, Martin Henriksson, Linköping University/AstraZeneca, Sweden
15.05-15.30
Coffee
15.30-16.30
Closing panel debate "Differences, similarities, and mergings
of model-based and network approaches to systems medicine"*
*Some 3-5 speakers from both of the days, moderated by Mikael Benson and Gunnar
Cedersund
Monday Dec 3, Workshop, diagnosis on the liver – in IMT1
Modelling of fluxes to aid radiologists
9.15-9.30 Olof Dahlqvist Leinhard, Linköping. Presentation of the Centre for Medical Image
Analysis and Visualisation (CMIV)
9.30-9.50 Bengt Noren, Linkoping. Needs and possibilites from a radiologists perspective
9.50-10.15 Mikael Forsgren and Gunnar Cedersund, Linkoping. A top-level flux-model as a
link between mechanistic multi-level modelling and clincial end-usage
10.15-10.45 Jose Ulloa, AstraZeneca, GB. PKPD-models for liver contrast agent fluxes in rats
10.45-11.15
Coffee
Modelling of liver metabolism
11.15-11.35 Mattias König, Berlin. Kinetic Modeling of Human Hepatic Glucose Metabolism
in T2DM.
11.35-12.00 Natal van Riel, Eindhoven. Kinetic models for Hepatic Mitocondrial Metabolism
in health and type 2 diabetes
12.00-13.30
Lunch
Modelling for surgical applications
13.30-13.50 Per Sandström, Linköping. Needs and possibilites from a surgeon's persective.
13.50-14.20 Andrea Schenk, MEVIS, Bremen, DE. Image-based liver surgery planning.
14.20-14.45 Peter Lundberg, Linköping, An non-invasive study of liver function during
regrowth following partial liver resection
14.45-15.15
Coffee
15.00-16.00
Final Panel Debate
Tuesday Dec 4: Modelling of diabetes, part 2, day 1
9-10: Peter Lundberg, Linköping, Usage of NMR to measure muscle and liver metabolism
(IMT1)
10-11: Björn Quistorff, Copenhagen, Muscle and brain metabolism (IMT2)
11-12: Natal van Riel, Eindhoven, The Netherlands, Models of muscle and liver metabolism
(IMT2)
Lunch
13.15-16: Hands-on session, Cont from part 1 and/or models of muscle and liver metabolism
(IMT11)
13.15-16: Tour to CMIV
16-17 Student presentations (IMT1)
Wednesday Dec 5: Modelling of diabetes, part 2, day 2
9-10: Mattias König, Berlin, A multi-level module for liver metabolism (IMT1)
10-11: Morten Gram Pedersen, Padova, A multi-level model for beta cell insulin secretion
(IMT1)
11-12: Lena Eliasson, Lund, Experimental work on beta cell insulin secretion (IMT1)
Lunch
13.15-16: Hands-on session, Cont from part 1 and/or models of liver and beta cell
metabolism (IMT11)
13.15-16: Tour to CMIV
16-17 Fredrik Nyström, Linköping, Planning and execution of clinical studies for type 2
diabetes, (IMT1)
FINAL PARTY
Thursday Dec 6: Going home day
9-12 Buffer time, probably not used (IMT1)
Note that the above schedule still is preliminary. An updated version is available at
http://isbgroup.eu/2012/