Tutorial: Modelling and Simulation Tools in Systems Biology

Singapore
Wednesday, November 25th, 2015 (9:00 - 18:00)


This tutorial workshop is a satellite of the 16th International Conference on Systems Biology (ICSB).
Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats.

The topics will include:

• Model setup using different software tools and systems biology platforms
• Using experimental data for setting up quantitative models
• Parameter estimation, optimization and model fitting
• Simulation, analysis and visualization of biochemical models
• Database supported modelling: integrated data management and model databases
• Community standards and formats for systems biology models
  
  

Target audience
Experimentalists and modellers with some basic experience in modelling and simulation of biological networks.

Location

Singapore
Yong Loo Lin School of Medicine, National University of Singapore (NUS)
Block MD1 - MD1-08-01E

Registration

Registration is possible through ICSB registration

Tutors

• Vijayalakshmi Chelliah: BioModels Team, EMBL-EBI (Cambridge, UK)
• Emek Demir: Oregon Health & Science University (Portland, OR, USA)
• Akira Funahashi and Noriko Hiroi: Keio University (Yokohama, Japan)
• Martin Golebiewski and Antonia Stank: Heidelberg Institute for Theoretical Studies (Germany)
• Pedro Mendes: University of Connecticut Health Center (Farmington, CT, USA)
• Sven Sahle and Jürgen Pahle: University of Heidelberg (Germany)
• Dagmar Waltemath and Martin Scharm: University of Rostock (Germany)

Agenda

Download Agenda

Covered tools and platforms

• CellDesigner: http://www.celldesigner.org/
  
• COPASI: http://www.copasi.org
  
• CombineArchive Toolkit: https://sems.uni-rostock.de/projects/combinearchive/
  
• LigDig: http://mcm.h-its.org/ligdig/
  
• SEEK: http://fair-dom.org/seek
  
• SYCAMORE: http://sycamore.eml.org
  
• webPIPSA: http://pipsa.h-its.org/
  

Covered standards

• BioPAX:http://www.biopax.org
  
• CellML:http://www.cellml.org/
  
• SBGN: http://www.sbgn.org
  
• SBML: http://sbml.org
  
• SED-ML: http://sed-ml.org/
  
• SBOL: http://sbolstandard.org
  

Covered databases

• BioModels database: http://www.ebi.ac.uk/biomodels-main/
  
• SABIO-RK: http://sabio.h-its.org/
  
  
  

Preparation

Attendees are expected to bring their own computer for hands-on training.

Please download these instructions for the SYCAMORE/webPIPSA/LigDig hands-on training

In order to profit best from the offered training you should pre-install the following software:

CellDesigner

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, and simulate and view the dynamics through an intuitive graphical interface. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi.
Download and Install CellDesigner 4.4

COPASI

COPASI is a software tool for handling, simulating, and analysing kinetic models of biochemical reaction networks. It is intended for biologists who are not experts in numerical algorithms or programming languages. The tutorial will give an overview over the features of COPASI, such as deterministic and stochastic simulation, parameter scans, sensitivities and control analysis. It will then focus on parameter estimation. We will provide model files for download in this space, so if you want to follow along the presentation on your own computer, please download the latest COPASI version 4.16 (Build 104) from the website www.copasi.org and install it on your computer.


You should also have a look at these online tools, databases and data management systems that will be introduced in detail during the tutorial workshop:

BioModels database

http://www.ebi.ac.uk/biomodels-main/

BioModels Database serves as a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided.

SABIO-RK

http://sabio.h-its.org/

SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. The data is either manually extracted from published literature or directly submitted by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK enables the access to kinetic data for experimentalists and modellers, supporting the setup of quantitative computer models.

SEEK

http://seek4science.org/

SEEK is a web-based platform, with associated tools, for finding, sharing and exchanging data, models and processes in Systems Biology. It is designed as data management platform to support systems biology consortia and distributed research networks. It is used, among others, in the European SysMO (Systems Biology of Microorganisms) consortium (http://www.sysmo-db.org/), as well as in the German Virtual Liver Network (http://seek.virtual-liver.de/)

SYCAMORE

http://sycamore.eml.org/

SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations. SYCAMORE is not intended to substitute for expert simulation and modeling software packages, but might interact with those. It is rather intended to support and guide system biologists when doing computational research.

PIPSA

http://pipsa.h-its.org

PIPSA (Protein Interaction Property Similarity Analysis) provides a service for comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties. PIPSA may assist in function assignment, the estimation of binding properties, and enzyme kinetic parameters. PIPSA can be downloaded or applied via the webPIPSA service.

LigDig

http://mcm.h-its.org/ligdig/

LigDig is a webserver for querying protein-ligand inter­actions and currently consists of seven tools. LigDig has been designed in a modular, linked fashion and the tools allow a user to: (i) perform a free-text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) batch search for compound identifiers, (v) find structures of protein-ligand complexes, (vi) compare three-dimensional structures of ligand binding sites, and (vii) prepare coordinate files of protein-ligand complexes for further calculations.

Organization