SysMod SIG 2016

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Advances in genomics are creating new opportunities to integrate systems modeling and bioinformatics. The goal of the first SysMod meeting was to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. The meeting covered qualitative and quantitative approaches as well as dynamical and steady-state modeling.

The meeting took place July 9, 2016 at the ISMB Conference in Orlando, Florida.

News: Congratulations to Benjamin Gyori for winning awarded the best poster of the first SysMod meeting. Ben received a $100 Amazon voucher.

Keynote speakers

Session 1: Modeling metabolism: from kinetics to the whole genome

Over the past 20 years flux balance analysis together with whole-genome sequencing have enabled researchers to construct detailed genome-scale models of metabolism. More recently, researchers have integrated transcriptomics and proteomics data into flux balance analysis models to generate more accurate predictions. This session featured two keynote talks on the state-of-the-art of genome-scale modeling, how it can be enhanced through combination with genomic data, and its prospects for precision medicine and microbial engineering.

Nathan Price.thumb.png Vassily Hatzimanikatis.thumb.png
Nathan Price Vassily Hatzimanikatis
Institute for Systems Biology and University of Washington, USA École polytechnique fédérale de Lausanne, Switzerland

Session 2: Pushing the boundaries of modeling

"Classical" dynamical modeling relies on the enumeration of biochemical components and processes, as well as large numbers of quantitative parameters. However, this information is often difficult to obtain. In addition, covalent modifications and assemblies of macromolecules cause a combinatorial explosion of states which is intractable to traditional methods. Several approaches have been designed to overcome these shortcomings and take advantage of the information that is available. This session featured a keynote talk from a researcher who has been instrumental in developing these methods and using them to analyze genome-scale data.

Ioannis Xenarios.thumb.png
Ioannis Xenarios
Swiss Institute of Bioinformatics, Switzerland

Contributed presentations and posters

The meeting will feature 8 contributed presentations and 10 contributed posters. The contributed abstracts are available here.


08:45-09:00 Welcome
Session 1: Modeling metabolism: from kinetics to whole genome
09:00-09:50 Metabolic analyses in microbes and humans
Nathan Price; Institute for Systems Biology, USA
09:50-10:15 First-principles modeling of metabolism using statistical thermodynamics and maximum entropy
Garrett Goh; Pacific Northwest National Laboratory, USA
10:15-10:45 Coffee break
10:45-11:10 An ensemble approach to unravel the design principles of cancer metabolic rewiring
Chiara Damiani; SYSBIO Centre of Systems Biology, Italy
11:10-11:35 Mighty morphing metabolic models: leveraging manual curations for automatic metabolic reconstruction of clades
Matthew Richards; Institute for Systems Biology, USA
11:35-12:00 Recent software and services to support the SBML community
Michael Hucka; California Institute of Technology, USA
12:00-12:50 Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
Vassily Hatzimanikatis; École polytechnique fédérale de Lausanne, Switzerland
Lunch and poster session
Session 2: Pushing the boundaries of modeling
13:40-14:05 High-performance computing in Systems Biology: accelerating the simulation and analysis of large and complex biological systems
Giancarlo Mauri; Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
14:05-14:40 The ZBIT systems biology software and web service collection
Andreas Dräger; Center for Bioinformatics Tuebingen, Germany and University of California, San Diego, USA
14:40-15:05 Systematic multi-scale modeling and analysis for gene regulation
Daifeng Wang; Yale University, USA
15:05-15:30 Rule-based modelling of clathrin polymerisation
Anatoly Sorokin; Institute of Cell Biophysics, Russia
15:30-16:00 Coffee break
16:00-16:50 From biocuration to model predictions and back
Ioannis Xenarios; Swiss Institute of Bioinformatics, Switzerland
16:50-17:15 Discussion and Q&A “Bioinformatics and modeling, bridging the divide”
17:15-17:30 Poster prize: Benjamin M. Gyori Harvard Medical School


Date and location

  • Date: Saturday July 9, 2016
  • Location: Room Pelican 1 of the Swan Hotel, 1500 Epcot Resorts Blvd, Walt Disney World, Lake Buena Vista, Florida, USA. Posters will be in the Swan ballrooms.

Key dates

  • March 28, 2016: ISMB registration opens
  • April 2, 2016: SysMod abstract submission deadline
  • April 17, 2016: Extended SysMod abstract submission deadline
  • April 29, 2016: SysMod oral and poster acceptance notification
  • May 10, 2016: SysMod program available online
  • June 2, 2016: ISMB early registration deadline
  • June 24, 2016: ISMB online registration deadline
  • July 7, 2016: ISMB on site registration opens
  • July 9, 2016: SysMod meeting
  • July 10-12, 2016: ISMB conference
  • July 10, 2016: Combined NetBio and SysMod COSI session

View as Google calendar | Download .ics

Organizing committee


The organisers are grateful for the support of the organisations below

BioPathways-Logo.png Merrimack Logo.png NPJ-SBA-logo.jpg
SysMod inherited funds from the former BioPathway SIG,

that was coordinated by Erich Bornberg-Bauer, Vincent Danos,
Janine Hatchwell, Toni Kazic, Joanne S. Luciano, Eric Neumann,
Aviv Regev, Frank Schacherer, Vincent Schächter.

More information

For more information, please contact