COMBINE & ERASysAPP Tutorial
COMBINE & ERASysAPP Tutorial
Modelling and Simulation of Biological Models
Date: Sunday, September 14th, 2014 (9:00 - 18:00)
Venue: To be advised (in the vicinity of the ICSB venue)
Participants will learn setting-up computer models of biological networks and simulating them in different systems biology platforms, as well as using databases and applying modelling standards. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills.
- 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
Standards (http://co.mbine.org/): CellML, SBGN, SBML, SED-ML
Databases: BioModels, JWS Online, Physiome Repository, SABIO-RK, SEEK
Modelling tools: CellDesigner, COPASI, OpenCOR, SBGN-ED, SYCAMORE, Virtual Cell
Experimentalists and modellers with basic experience in modelling and simulation
- Akira Funahashi and Noriko Hiroi: Keio University (Yokohama, Japan)
- Martin Golebiewski: Heidelberg Institute for Theoretical Studies (Germany)
- Mike Hucka: California Institute of Technology (Pasadena, CA, USA)
- Ursula Kummer and Jürgen Pahle: University of Heidelberg (Germany)
- Nicolas Le Novère: Babraham Institute (Cambridge, UK)
- Ion Moraru: University of Connecticut Health Center (Farmington, CT, USA)
- David Nickerson: Auckland Bioengineering Institute (New Zealand)
- Falk Schreiber: Monash University (Melbourne, Australia)
- Jacky Snoep: Stellenbosch University (South Africa)
- Natalie Stanford: University of Manchester (UK)
HITS gGmbH, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
STRENDA Special Issue
Special Issue: Reporting Enzymology Data – STRENDA Recommendations and Beyond – a highly educational, open access collection of 14 articles (published May 2014)
The STRENDA (Standards for Reporting Enzymology Data) Commission was set up almost ten years ago to address the improvement of the reporting quality of functional enzyme data in order to support the community with the efficient application of enzyme kinetics in the investigation of biological systems in vivo, in vitro and in silico. The Commission proposes guidelines as to how functional enzyme data should be described in the literature, with a detailed checklist of information, such as an unambiguous identification of the enzyme, a description of its preparation and of the conditions under which it was assayed. Experts from a wide range of specific research areas within enzymology were invited to add their views on, for example, thermodynamics, isotope effects, application of NMR, development and application of enzyme nomenclature, methods in designing enzyme assays in basic research and industrial biocatalysis as well as on the issues of data capturing, storage and mining in databases. This open access collection of 14 articles is addressed to all readers, including students, researchers and professors, who are interested in general aspects of data quality and in ways to interpret already published data.
Computational data in SABIO-RK
In February 2014 SABIO-RK started to include in silico data from computational models. The search can be defined by selecting the filtering option "BioModel".
Data are uploaded via SBML format and linked to the original source e.g. BioModels Database.
Signalling data in SABIO-RK
With the release 2013_08 it is now possible to search SABIO-RK for kinetic data related to signalling reactions. You can either search for participating molecules, a signalling modification or a signalling event. Naturally, any other search possibility is also supported as for the metabolic reactions.
SABIO-RK tutorial at ICSB 2013
A SABIO-RK tutorial will be presented as part of a full-day tutorial workshop on September 4, 2013 following the ICSB conference in Copenhagen (Denmark).
Detailed information can be found at the conference homepage:
ICSB workshop programme
UniProt links to SABIO-RK
Starting with the release 2013_03 UniProtKB contains cross-references to SABIO-RK within "Enzyme and pathway databases". Currently, 2983 UniProt accession numbers link to kinetic data in SABIO-RK.
UniProt release 2013_03