SysMod ISMB 2017

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The second SysMod meeting took place on Saturday July 22nd 2017, as part of the ISMB 2017 conference in Prague.

The meeting featured invited keynotes, selected oral presentations and posters (as part of ISMB 2017 poster sessions). Oral presentations were selected based on abstracts submitted to SysMod, or articles submitted to the ISMB Proceedings.


Rainer Breitling.png
Prof Rainer Breitling studied biochemistry at the University of Hannover, Germany, and received his Ph.D. from the Technical University of Munich, Germany, in 2001. He held postdoctoral positions as a bioinformatician at San Diego State University (California, USA) and the University of Glasgow (UK), followed by professorial appointments at the University of Groningen (The Netherlands) and the University of Glasgow. Since September 2012 he is Professor of Systems Biology at the Manchester Institute of Biotechnology, University of Manchester. The Breitling group is interested in using computational approaches to understand complex biological systems, ranging from microbes to man. They develop methods to interpret “molecular profiles”, e.g., the global patterns of gene expression or the abundance of small molecules (metabolites) in biological samples. In addition they develop quantitative models to describe and predict the behaviour of cells, e.g., after drug treatment or genetic manipulation. More about Rainer Breitling's research can be found on his webpage and his Google Scholar profile.
Jana Wolf Portrait.jpg
Dr Jana Wolf studied biophysics at the Humboldt University in Berlin, Germany, where she received her PhD in 2000. She pursued post-doctoral research at the GlaxoSmithKline Medicines Research Centre, UK. Since 2008, she is group leader in Mathematical Modelling of Cellular Processes at the Max Delbrück center for molecular medicine in Berlin. Dr Wolf's group develops and analyses mathematical models of signalling pathways and gene-regulatory networks in normal and disease states. For their investigations they use tools such as simulations, bifurcation analyses and sensitivity analyses. These give insights into the dynamical properties of the systems and help to identify most sensitive processes and critical regulations. Another important aspect is the investigation of cell specific differences in signalling and gene-regulatory networks since these are critically involved in the prediction of the efficiency and possible side-effects of drugs. More about Jana Wolf's research can be found on her webpage.

Presentations at SysMod 2017

Oral presentations will feature invited speakers, as well as speakers selected from proceedings and abstracts. Selected proceedings will be published in the journal Oxford Bioinformatics. All posters and slides will subsequently be published - if the presenters wish so - in the F1000Research ISCB Journal.

TThe list of selected presentations can be found at: SysMod_ISMB_2017_Abstracts


Date and location

  • Date: Saturday July 22nd, 2017
  • Location: Prague Convention Center, room panorama

Key dates

  • Monday, December 19, 2016: Proceedings submission opens
  • Thursday, January 3, 2017: Abstract submission opens
  • Thursday, January 26, 2017: Proceedings submission deadline
  • Tuesday, February 28, 2017: Proceedings acceptance notification
  • Thursday, April 6, 2017: Revised proceedings submission deadline
  • Thursday, April 13, 2017: Abstract submission deadline
  • Thursday, April 20, 2017: Final proceedings acceptance notification
  • Friday, May 12, 2017: Abstract acceptance notification
  • July 21-25, 2017: ISMB conference
  • Saturday, July 22, 2017: SysMod COSI sessions

Registrations and fees

The SysMod meeting is now an integral part of the ISMB. People interested to attend registered through ISMB. 2-days and 4-days registrations were available.


10:00-12:30 Session 1: “Stochastic, Bayesian, and Logical Modeling” chaired by Nicolas Le Novère
10:00-10:50 Keynote talk: Modeling in uncertain times
Rainer Breitling; University of Manchester, UK
10:50-11:10 Proceedings paper (Bioinformatics) - A scalable moment-closure approximation for large-scale biochemical reaction networks
Atefeh Kazeroonian; Helmholtz-Zentrum München, DE
11:10-11:30 Proceedings paper (Bioinformatics) - Efficient Simulation of Intrinsic, Extrinsic and External Noise in Biochemical Systems
Dennis Pischel; Max Planck Institute for Dynamics of Complex Technical Systems, DE
11:30-11:50 Proceedings paper (Bioinformatics) - Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
Eugenio Cinquemani; INRIA Grenoble, FR
11:50-12:10 Reversed dynamics to uncover basins of attraction of asynchronous logical models
Claudine Chaouiya; Instituto Gulbenkian de Ciência, PT
12:30-14:00 Lunch
14:00-16:00 Session 2: “Disease and Cancer Modeling” chaired by Laurence Calzone
14:00-14:50 Keynote talk: Computational modeling of promoter occupancies in MYC-dependent gene regulation
Jana Wolf; Max Delbrück center for molecular medicine, Berlin, DE
14:50-15:10 Manatee invariants for functional analysis of signaling pathways in complex networks
Ina Koch;Johann Wolfgang Goethe-University, Frankfurt am Main, DE
15:10-15:30 Large Scale Mechanistic Modeling Enables Robust Prediction of Cancer Cell Drug Response
Fabian Fröhlich; Helmholtz-Zentrum München, DE
15:30-15:50 Incorporating patient-specific molecular data into a logic model of prostate cancer
Pauline Traynard; Institut Curie, Paris, FR
16:00-16:30 Coffee break with exhibitors
16:30-18:00 Session 3: “Flux Balance Analysis, Genome-Scale, and Whole-Cell Modeling” chaired by Andreas Dräger
16:30-16:50 Proceedings paper (Bioinformatics) - popFBA: tackling intratumour heterogeneity with Flux Balance Analysis
Chiara Damiani; Department of Informatics, Systems and Communication University of Milan Bicocca, IT
16:50-17:10 Who's driving? Cell cycle robustness investigated by a multi-scale framework integrating cell cycle and metabolism in budding yeast
Matteo Barberis; Universiteit van Amsterdam, NL
17:10-17:30 Explanation of drug effects using a mechanistic model automatically assembled from natural language, databases, and literature
John A. Bachman; Harvard Medical School, USA
17:30-17:50 Tracking and Engineering the Evolution of Organismal Fitness via Multi-Organism mRNA Translation Whole Cell Simulations
Tamir Tuller; Tel Aviv University, IL
18:00-19:00 Poster presentations