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Seminar 14481
Multiscale Spatial Computational Systems Biology

David Gilbert (Brunel University, GB), Monika Heiner (BTU Cottbus, DE), Koichi Takahashi (Osaka University, JP), Adelinde M. Uhrmacher (Universität Rostock, DE)

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Seminar Wide Materials
 
 


Steven Andrews , Frederic Hutchinson Cancer Center - Seattle
 Steve 3 min talk
Slides: pdf

 Smoldyn software
Slides: pdf

 Crowding papers
Slides: zip

 Crowding case study final presentation
Slides: pdf

 

Satya Arjunan , Osaka University
 3 min intro
Slides: pdf

 

Gianfranco Balbo , University of Turin
 Unito presentation
Slides: pdf

 

Ezio Bartocci , TU Wien
 3 min presentation
Slides: pdf

 

Marco Beccuti , University of Turin
 

Arne Bittig , Universität Rostock
 3 min intro - A rule based language and spatial simulation
Abstracts: txt Slides: pdf

 Case Study: Mitochondrial Networks and Health
Slides: pptx

 ML-Space Model Reader & Simulator (Java)
Other: zip

 ML-Space simulation results for Crowding experiment
Slides: pdf

 

Mary Ann Blaetke , Universität Magdeburg - IBIO
 Modular Biomodel-Engineering
Slides: pdf

 Case-Study: Dictyostelium
Slides: pdf

 Progress Report: Dictyostelium - Aggregation and Synchronisation in Space
Slides: pdf

 Final Report: Dictyostelium - Aggregation and Synchronisation in Space
Slides: pptx

 

Luca Bortolussi , Universität des Saarlandes
 3 minutes short overview
Slides: pdf

 Case Study: spatial segregation of small-GTPase
Slides: pdf

 

Lutz Brusch , TU Dresden
 3min introduction
Slides: pdf

 

Alfonso Bueno-Orovio , University of Oxford
 3min presentation
Slides: pdf

 

Kevin Burrage , University of Oxford
 Multiscale modelling
Other: pdfpdfpdf

 Group 2 report
Slides: pptxpdf

 

Francesca Cordero , University of Turin
 

Andreas Deutsch , TU Dresden
 personal presentation Andreas Deutsch
Slides: pdf

 

Maciej Dobrzynski , University College - Dublin
 

Dirk Drasdo , INRIA - Le Chesnay
 Group on Multi-Cellular Systems Biology
Slides: pptx

 Multi-cellular Systems Biology and Medicine
Abstracts: txt Paper: pdfpdfpdfpdf

 

Radek Erban , University of Oxford
 3 minute slides
Slides: pdf

 working report
Other: pdf

 

Martin Falk , Linköping University
 Mesoscopic Simulation and Visualization in Systems Biology
Slides: pdf

 

Flavio Fenton , Georgia Institute of Technology
 3 min talk
Slides: pdf Other: pdf

 

Jerome Feret , ENS - Paris
 3 minutes overview
Slides: pdf

 Model of crowding in Kappa
Slides: pdf Other: kaout

 

Chiara Fornari , University of Turin
 

Akira Funahashi , Keio University
 3 minutes overview
Slides: pdf

 

Anna Gambin , University of Warsaw
 A. Gambin research
Slides: pdf

 Sphingolipids metabolism case study
Slides: pdf

 model
Slides: jpg

 

David Gilbert , Brunel University - London
 Multiscale Modelling Challenges in Biology
Slides: pptx Paper: pdf

 3 minute publicity
Slides: pdf

 

Simon Hardy , Université Laval - Québec
 3 min presentation
Abstracts: txt

 dictyostelium wave models
Other: xml

 dictyostelium_movement model
Other: xml

 

Monika Heiner , BTU Cottbus
 From Petri Nets to PDEs in 3 minutes
Abstracts: txt Slides: pdf

 

Mostafa Herajy , Port Said University
 Computational Steering of Multiscale Models
Abstracts: txt Slides: pdf

 

Dagmar Iber , ETH Zürich - Basel
 PDE Models methods talk
Slides: pdfpptx

 Results Optimization
Slides: pdfpptx

 

Kazunari Kaizu , RIKEN Quantitative Biology Center - Osaka
 

Andrzej M Kierzek , University of Surrey
 

Tetsuya J Kobayashi , University of Tokyo
 

Marek Kochanczyk , Polish Academy of Sciences - Warsaw
 Research overview (3-min)
Slides: pdf

 

Fei Liu , Harbin Institute of Technology
 Colored Petri Nets for Multiscale Modeling of Biological Systems
Slides: pdf

 Colored Petri Nets for Multiscale Systems Biology
Abstracts: txt Paper: doc

 

Guillaume Madelaine , University of Lille I
 Attractor Equivalence, short talk
Slides: pdf

 

Wolfgang Marwan , Universität Magdeburg - IBIO
 3 minutes Overview
Slides: pdf

 

Carsten Maus , DKFZ - Heidelberg
 3 minute introduction
Slides: pdf

 

Sebastian Naehring , Universität Rostock
 

Joachim Niehren , INRIA - University of Lille 1
 Gene Knockout Prediction by Abstract Interpretation
Abstracts: txt

 3 minutes presentation
Slides: pdf

 

Ovidiu Parvu , Brunel University
 Short presentation of my research (3 minutes)
Slides: pptxpdf

 Coloured Petri Nets Methods Presentation
Abstracts: txt Slides: pptxpdf

 

Christian Rohr , BTU Cottbus
 3min short introduction
Slides: pdf

 

Guido Sanguinetti , University of Edinburgh
 3 min presentation
Abstracts: txt Slides: pdf

 talk on spatio-temporal smoothing
Abstracts: txt Slides: pdf

 PNAS paper on afghanistan modelling
Other: pdf

 IEEE Trans Sign Proc paper on spatio-temporal data inference
Other: pdf

 QEST paper on using GP-UCB for inference of parameters of stochastic processes
Other: pdf

 draft team report for team2
Paper: pdf Other: tex

 

Koichi Takahashi , Osaka University
 

Yuichi Togashi , Hiroshima University
 Spying “Minorities” in the Cell (full version)
Slides: ppt

 Spying “Minorities” in the Cell in 3 minutes
Slides: pdf

 Case Study: Structural Dynamics of DNA at Multiple Scales
Slides: pdf

 Team 5 progress (DNA Structural Dynamics)
Slides: pptxpdf

 Memo for Team 5
Other: pdf

 

Adelinde M Uhrmacher , Universität Rostock
 

Walter de Back , TU Dresden
 3 min pitch: Multicellular systems biology of development
Slides: pdf

 Case study: Vascular network formation
Slides: pdf

 Case: Standard exchange format
Slides: pdf

 



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