de.NBI ModSim

Resources, Services and Developments for Systems Biology Modeling

Partner project of the German Network for Bioinformatics Infrastructure (de.NBI)

About de.NBI ModSim


Resources, Services and Developments for Systems Biology Modeling.


de.NBI-ModSim is a partner project of de.NBI-SysBio node and has three major goals:

  1. Adding new resources to de.NBI: in particular, COPASI and CellNetAnalyzer, two complementary and frequently used software packages for modeling biological networks and systems will be promoted by de.NBI-ModSim.
  2. Providing services: extended user support and organization of workshops and training courses on mathematical modeling of biological systems including hands-on exercises with the software tools
  3. de.NBI-relevant developments: for example, integration of COPASI and CellNetAnalyzer with existing resources of de.NBI and make these tools compliant with model standardization and annotation schemes propagated by the de.NBI-SysBio node.

More about de.NBI

 

de.NBI

Events


The following events are scheduled for 2023:

  • 28. - 30. Nov, 2023: 3-day virtual workshop (with CellNetAnalyzer, COPASI and SABIO RK hands-on exercises) more information | registration

The following events are scheduled for 2022:

The following events are scheduled for 2021:

  • 20. - 22. Apr, 2021: 3-day virtual workshop (with CellNetAnalyzer, COPASI and SABIO RK hands-on exercises) more information | registration

The following events are scheduled for 2020:

  • 21. - 23. Sep, 2020: 3-day virtual workshop (with CellNetAnalyzer, COPASI and SABIO RK hands-on exercises) more information | registration
  • CANCELLED 27. - 29. April, 2020: 3-day workshop in Magdeburg (with CellNetAnalyzer, COPASI and SABIO RK hands-on exercises) more information

The following events are scheduled for 2019:

The following events are scheduled for 2018:

The following events are scheduled for 2017:

  • 12. / 13. September, 2017: 2-days workshop (with COPASI and CellNetAnalyzer hands-on exercises) more information
  • August 6, 2017:joint COMBINE Tutorial ICSB 2017 (Blacksburg, VA) more information
  • August 7, 2017:Advanced COPASI Tutorial at ICSB 2017 (Blacksburg, VA)

COPASI

COPASI is a software tool for editing, simulating, and analyzing models of biochemical reaction networks. COPASI is available for all major platforms (Linux, Windows, OS X), easy to install COPASI is free and open source software.

COPASI Website User Forum


Features

  • ODE-based and stochastic formalisms
  • Sensitivity analyses
  • Optimization and parameter estimation
  • Computation of stable states and properties of nonlinear, dynamical systems, e.g. Lyapunov exponents
  • Hybrid simulation methods
  • Model ­reduction techniques
  • Further properties:
  • COPASI is SBML compatible
  • Standards, e.g. for model annotations are implemented

A complete list of features is available on the COPASI website.

Usage of COPASI - global view

COPASI - global usage map

Note: only approx. 30% of the publications, having used COPASI have been included so far. For more information see the live page .

Support

Training


CellNetAnalyzer

CellNetAnalyzer (CNA) is a MATLAB toolbox providing a graphical user interface and various (partially unique) computational methods and algorithms for exploring structural and functional properties of metabolic, signaling, and regulatory networks.

CNA Website User Forum


Features

Numerous methods and algorithms from stoichiometric and constraint-based modeling:

  • conservation relations
  • metabolic flux analysis
  • flux balance analysis (FBA) / flux optimization
  • flux variability analysis
  • elementary-modes and pathway analysis
  • minimal cut sets (design/redesign of metabolic networks)
  • SBML import / export

Support for influence graphs / boolean networks including :

  • logical steady-sate analysis (qualitative I/O behvaior)
  • minimal intervention sets
  • feedback loops and signaling paths
  • global interdependency of species
  • data-driven inference of signaling network toplogies
  • simulation of logic-based ODEs (ODEfy)
  • Support of the SBML Level 3 Qual extension

for a detailed description of CellNetAnalyzer's capabilities please see the CNA website.

Usage of CellNetAnalyzer - global view

CellNetAnalyzer - global usage map

Support

Training


Screen Shots


timecourse simulation in COPASI

Model overview / time course simulation in COPASI

constraint-based modelling in CellNetAnalyzer

stoichiometric / constraint-based modelling in CellNetAnalyzer

influence graphs / boolean networks in CellNetAnalyzer

influence graphs / boolean networks in CellNetAnalyzer




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Contact

Prof Dr. Ursula Kummer

INF 267
69120 Heidelberg

ursula.kummer @ bioquant.uni-heidelberg.de

Steffen Klamt

Max Planck Institute for Dynamics of Complex Technical Systems
Sandtorstr. 1
D-39106 Magdeburg Germany

klamt @ mpi-magdeburg.mpg.de